Powerful MHC-class II peptides derived from survivin

ABSTRACT

The present invention relates to peptides, nucleic acids, and cells for use in the immunotherapy of cancer. The present invention furthermore relates to survivin-derived tumor-associated cytotoxic T cell (CTL) peptide epitopes, alone or in combination with other tumor-associated peptides that serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses. The present invention specifically relates to three novel peptide sequences and variants thereof derived from HLA class I and class II molecules of human tumor cells that can be used in vaccine compositions for eliciting anti-tumor immune responses.

RELATED APPLICATIONS

This application is a Continuation of U.S. application Ser. No.12/466,222, filed May 14, 2009, and issued as U.S. Pat. No. 8,647,629 onFeb. 11, 2014, which claims priority to U.S. Provisional Application No.61/053,182, filed on May 14, 2008 and EP application 08 008944.4, filedon May 14, 2008, each of which is herein incorporated by reference inits entirety.

FIELD OF THE INVENTION

The present invention relates to peptides, nucleic acids, and cells foruse in immunotherapeutic methods. In particular, the present inventionrelates to the immunotherapy of cancer. The present inventionfurthermore relates to survivin-derived tumor-associated cytotoxic Tcell (CTL) peptide epitopes, alone or in combination with othertumor-associated peptides that serve as active pharmaceuticalingredients of vaccine compositions that stimulate anti-tumor immuneresponses. The present invention specifically relates to three novelpeptide sequences and variants thereof derived from HLA class I andclass II molecules of human tumor cells that can be used in vaccinecompositions for eliciting anti-tumor immune responses.

BACKGROUND OF THE INVENTION

Gliomas are brain tumors originating from glial cells in the nervoussystem. Glial cells, commonly called neuroglia or simply glia, arenon-neuronal cells that provide support and nutrition, maintainhomeostasis, form myelin, and participate in signal transmission in thenervous system. The two most important subgroups of gliomas areastrocytomas and oligodendrogliomas, named according to the normal glialcell type from which they originate (astrocytes or oligodendrocytes,respectively). Belonging to the subgroup of astrocytomas, glioblastomamultiforme (referred to as glioblastoma hereinafter) is the most commonmalignant brain tumor in adults and accounts for approximately 40% ofall malignant brain tumors and approximately 50% of gliomas (CBTRUS,2006). It aggressively invades the central nervous system and is rankedat the highest malignancy level (grade IV) among all gliomas. Althoughthere has been steady progress in treatment due to improvements inneuroimaging, microsurgery, diverse treatment options, such astemozolomide or radiation, glioblastomas remain incurable (Macdonald,2001; Burton and Prados, 2000; Prados and Levin, 2000). The lethalityrate of this brain tumor is very high: the average life expectancy is 9to 12 months after first diagnosis. The 5-year survival rate during theobservation period from 1986 to 1990 was 8.0%. To date, the five-yearsurvival rate following aggressive therapy including gross tumorresection is still less than 10% (Burton and Prados, 2000; Nieder etal., 2000; Napolitano et al., 1999; Dazzi et al., 2000). Accordingly,there is a strong medical need for an alternative and effectivetherapeutic method.

Tumor cells of glioblastomas are the most undifferentiated cells amongbrain tumors. Thus, the tumor cells have high potential of migration andproliferation and are highly invasive, leading to very poor prognosis.Glioblastomas lead to death due to rapid, aggressive, and infiltrativegrowth in the brain. The infiltrative growth pattern is responsible forthe unresectable nature of these tumors. Glioblastomas are alsorelatively resistant to radiation and chemotherapy, and, therefore,post-treatment recurrence rates are high. In addition, the immuneresponse to the neoplastic cells is rather ineffective in completelyeradicating all neoplastic cells following resection and radiationtherapy (Roth and Weller, 1999; Dix et al., 1999; Sablotzki et al.,2000).

Glioblastoma is classified into primary glioblastoma (de novo) andsecondary glioblastoma, depending on differences in the gene mechanismduring malignant transformation of undifferentiated astrocytes or glialprecursor cells. Secondary glioblastoma occurs in a younger populationof up to 45 years of age. During 4 to 5 years, on average, secondaryglioblastoma develops from lower-grade astrocytoma throughundifferentiated astrocytoma. In contrast, primary glioblastomapredominantly occurs in an older population with a mean age of 55 years.Generally, primary glioblastoma occurs as fulminant glioblastomacharacterized by tumor progression within 3 months from the state withno clinical or pathological abnormalities (Pathology and Genetics of theNervous Systems. 29-39 (IARC Press, Lyon, France, 2000)).

Glioblastoma migrates along myelinated nerves and spreads widely in thecentral nervous system. In most cases surgical treatment shows onlylimited sustainable therapeutic effect (Neurol. Med. Chir. (Tokyo) 34,91-94, 1994; Neurol. Med. Chir. (Tokyo) 33, 425-458, 1993;Neuropathology 17, 186-188, 1997) (Macdonald, 2001; Prados and Levin,2000).

Malignant glioma cells evade detection by the host's immune system byproducing immunosuppressive agents that impair T cell proliferation andproduction of the immune-stimulating cytokine IL-2 (Dix et al., 1999).

Intracranial neoplasms can arise from any of the structures or celltypes present in the central nervous system (CNS), including the brain,meninges, pituitary gland, skull, and even residual embryonic tissue.The overall annual incidence of primary brain tumors in the UnitedStates is 14 cases per 100,000. The most common primary brain tumors aremeningiomas, representing 27% of all primary brain tumors, andglioblastomas, representing 23% of all primary brain tumors (whereasglioblastomas account for 40% of malignant brain tumor in adults). Manyof these tumors are aggressive and are of high grade. Primary braintumors are the most common solid tumors in children and the second mostfrequent cause of cancer death, after leukemia, in children.

The search for effective treatment of glioblastomas in patients is stillongoing today. Immunotherapy, or treatment via recruitment of the immunesystem, to fight these neoplastic cells has been investigated. Firstencouraging results were obtained by Northwest Therapeutics using “DCVaxBrain” for the treatment of glioblastoma in immuno-therapeutic studiesin humans, in which antigen-specific cytotoxic lymphocyte (CTL)responses could be induced leading to prolonged median survival timescompared to that obtained applying standard treatment. Further thistreatment was accompanied by minimal toxicity (Heimberger et al., 2006).

Colorectal Carcinoma

According to the American Cancer Society, colorectal cancer (CRC) is thethird most common cancer in the US, afflicting more than 175,000 newpatients each year. In the US, Japan, France, Germany, Italy, Spain andthe UK, it affects more than 480,000 patients. It is one of the mostcommon causes of cancer mortality in developed countries. The 1- and5-year relative survival for persons with colorectal cancer is 84% and64%, respectively. Survival continues to decline beyond 5 years. Forinstance at 10 years after diagnosis survival is 57%. When colorectalcancers are detected at an early, localized stage, the 5-year survivalis 90%; however, only 39% of colorectal cancers are diagnosed at thisstage, mostly due to low rates of screening. After the cancer has spreadregionally to involve adjacent organs or lymph nodes, the 5-yearsurvival drops to 68%. For persons with distant metastases, 5-yearsurvival is 10%.

Research suggests that the onset of colorectal cancer is the result ofinteractions between inherited and environmental factors. In most cases,adenomatous polyps appear to be precursors to colorectal tumors; howeverthe transition may take many years. The primary risk factor forcolorectal cancer is age, with 90% of cases diagnosed over the age of 50years. Other risk factors for colorectal cancer according to theAmerican Cancer Society include alcohol consumption, a diet high in fatand/or red meat and an inadequate intake of fruits and vegetables.Incidence continues to rise, especially in areas such as Japan, wherethe adoption of westernized diets with excess fat and meat intake and adecrease in fiber intake may be to blame. However, incidence rates arerising not as fast as previously, which may be due to increasingscreening and polyp removal, thus preventing progression of polyps tocancer.

As in most solid tumors, first line treatment is surgery, however, itsbenefits remain confined to early-stage patients. A significantproportion of patients are diagnosed in advanced stages of the disease.For advanced colorectal cancer chemotherapy, regimens based onfluorouracil-based regimens are standard of care. The majority of theseregimens are the so-called FOLFOX (infusional 5-FU/leucovorin plusoxaliplatin) and FOLFIR1 (irinotecan, leucovorin, bolus andcontinuous-infusion 5-FU) protocols.

The introduction of third-generation cytotoxics such as irinotecan andoxaliplatin has raised the hope of significantly improving efficacy, butprognosis is still relatively poor, and the survival rate generallyremains at approximately 20 months in metastatic disease and, as aresult, the unmet needs in the disease remain high.

Recently, a novel generation of drugs, molecular-targeted agents, suchas AVASTIN® (bevacizumab) and ERBITUX® (cetuximab), became available,and about 40 compounds are in late-stage clinical development fordifferent stages of colorectal cancer. Combinations of several of thesecompounds increase the number of potential treatment options to beexpected for the future. The vast majority of substances are in phaseII, with the EGFR being addressed by these compounds more often than anyother target in colorectal cancer trials, which is due to the fact thatin ˜80% of patients with colorectal cancer, EGFR expression isupregulated.

Clinical trials with stage II patients combining chemotherapy with therecently approved monoclonal antibodies (mAbs) (cetuximab+irinotecan orFOLFOX4; bevacizumab as a single-agent or together with FOLFOX4) arecurrently being conducted. Three to four year observation periods areexpected for statistically significant results from these trials.

Monoclonal antibodies (mAbs) presently used in oncology in general havean excellent chance of not interfering with active immunotherapy. Infact, there is preclinical (GABRILOVICH 1999) and clinical evidencesuggesting that depletion of VEGF (by bevacizumab) contributespositively to DC-mediated activation of T-cells (Osada T, Chong G,Tansik R, Hong T, Spector N, Kumar R, Hurwitz H I, Dev I, Nixon A B,Lyerly H K, Clay T, Morse M A. The effect of anti-VEGF therapy onimmature myeloid cell and dendritic cells in cancer patients. CancerImmunol Immunother. 2008 Jan. 10.).

Prostate Carcinoma and Other Tumors

With an estimated 27,050 deaths in 2007, prostate cancer is a leadingcause of cancer death in men. Although death rates have been decliningamong white and African American men since the early 1990s, rates inAfrican American men remain more than twice as high as those in whitemen. Prostate cancer is the most frequently diagnosed cancer in men. Forreasons that remain unclear, incidence rates are significantly higher inAfrican American men than in white men. Incidence rates of prostatecancer have changed substantially over the last 20 years: rapidlyincreasing from 1988-1992, declining sharply from 1992-1995, andincreasing modestly since 1995. These trends in large part reflectincreased prostate cancer screening with the prostate-specific antigen(PSA) blood test. Moderate incidence increases in the last decade aremost likely attributable to widespread PSA screening among men youngerthan 65. Prostate cancer incidence rates have leveled off in men aged 65years and older. Rates peaked in white men in 1992 (237.6 per 100,000men) and in African American men in 1993 (342.8 per 100,000 men).

Treatment for prostate cancer may involve watchful waiting, surgery,radiation therapy, High Intensity Focused Ultrasound (HIFU),chemotherapy, cryosurgery, hormonal therapy, or some combination. Thebest option depends on the stage of the disease, the Gleason score, andthe PSA level. Other important factors are the man's age, his generalhealth, and his feelings about potential treatments and their possibleside effects. Because all treatments can have significant side effects,such as erectile dysfunction and urinary incontinence, treatmentdiscussions often focus on balancing the goals of therapy with the risksof lifestyle alterations.

If the cancer has spread beyond the prostate, treatment optionssignificantly change, so most doctors who treat prostate cancer use avariety of nomograms to predict the probability of spread. Treatment bywatchful waiting, HIFU, radiation therapy, cryosurgery, and surgery aregenerally offered to men whose cancer remains within the prostate.Hormonal therapy and chemotherapy are often reserved for disease thathas spread beyond the prostate. However, there are exceptions: radiationtherapy may be used for some advanced tumors, and hormonal therapy isused for some early stage tumors. Cryotherapy, hormonal therapy, andchemotherapy may also be offered if initial treatment fails and thecancer progresses.

In a significant number of patients with prostate carcinoma who undergoradical prostatectomy because of clinically suspected organ-limitedgrowth, a definitive histological workup of the surgical preparationshows a locally extensive tumor extending beyond the borders of theorgan. These patients have a high risk for early local recurrence,usually detectable as increasing PSA level in terms of a biochemicalrelapse. Therapeutic options in this situation include externalradiotherapy and hormone ablation; however, the value of thesetherapeutic approaches, especially with respect to prolonging thepatient's long-term survival, must not be regarded as proven. Inaddition, possible treatment-associated complications such as thedevelopment of urethral strictures (radiotherapy), loss of libido andimpotence, the risk of a reduction in skeletal calcium salts in terms ofosteoporosis, and a markedly increased risk of pathologic bone fractures(hormone ablation) must be considered.

More than 90% of all prostate cancers are discovered in the local andregional stages; the 5-year relative survival rate for patients whosetumors are diagnosed at these stages approaches 100%. Over the past 25years, the 5-year survival rate for all stages combined has increasedfrom 69% to nearly 90%. According to the most recent data, relative10-year survival is 93% and 15-year survival is 77%. The dramaticimprovements in survival, particularly at 5 years, are partlyattributable to earlier diagnosis and improvements in treatment.Nevertheless, the survival rate drops significantly after spreading toother tissues and organs.

Lung Cancer

Estimated 210,000 new cases are expected in 2007 in the USA, accountingfor about 15% of cancer diagnoses. The incidence rate is decliningsignificantly in men, from a high of 102 cases per 100,000 in 1984 to78.5 in 2003. In women, the rate is approaching a plateau after a longperiod of increase. Lung cancer is classified clinically as small cell(13%) or non-small cell (87%) for the purposes of treatment.

Lung cancer accounts for the most cancer-related deaths in both men andwomen. An estimated 160,390 deaths, accounting for about 29% of allcancer deaths, are expected to occur in 2007. Since 1987, more womenhave died each year from lung cancer than from breast cancer. Deathrates have continued to decline significantly in men from 1991-2003 byabout 1.9% per year. Female lung cancer death rates are approaching aplateau after continuously increasing for several decades. These trendsin lung cancer mortality reflect the decrease in smoking rates over thepast 30 years.

Treatment options are determined by the type (small cell or non-smallcell) and stage of cancer and include surgery, radiation therapy,chemotherapy, and targeted biological therapies such as bevacizumab(AVASTIN®) and erlotinib (TARCEVA®). For localized cancers, surgery isusually the treatment of choice. Recent studies indicate that survivalwith early-stage, non-small cell lung cancer is improved by chemotherapyfollowing surgery. Because the disease has usually spread by the time itis discovered, radiation therapy and chemotherapy are often used,sometimes in combination with surgery. Chemotherapy alone or combinedwith radiation is the usual treatment of choice for small cell lungcancer. However with this regimen, a large percentage of patientsexperience remission, which is long lasting in some cases.

The 1-year relative survival for lung cancer has slightly increased from37% in 1975-1979 to 42% in 2002, largely due to improvements in surgicaltechniques and combined therapies. However, the 5-year survival rate forall stages combined is only 16%. The survival rate is 49% for casesdetected when the disease is still localized; however, only 16% of lungcancers are diagnosed at this early stage.

TABLE 1 Estimated new cancer cases and deaths by sex for the US in 2007(American Cancer Society. Cancer Facts & Figures 2007. Atlanta: AmericanCancer Society; 2007.) Estimated New Cases Estimated Deaths Sites BothSexes Male Female Both Sexes Male Female Glioma and Brain 20,500 11,1709,330 12,740 7,150 5,590 Breast 180,510 2,030 178,480 40,910 450 40,460Prostate 218,890 218,890 27,050 27,050 Esophagus 15,560 12,130 3,43013,940 10,900 3,040 Colon 112,340 55,290 57,050 52,180 26,000 26,180Renal 51,190 31,590 19,600 12,890 8,080 4,810 Pancreas 37,170 18,83018,340 33,370 16,840 16,530 Squamous cell 1,000,000 n.d. n.d. n.d. n.d.n.d. carcinomas; Keratinocytic neoplasms of the skin Leukemia 44,24024,800 19,440 21,790 12,320 9,470 Lung 213,380 114,760 98,620 160,39089,510 70,880 Non-Hodgkins 63,190 34,210 28,990 18,660 9,600 9,060Lymphoma Ovarian 22,430 22,430 15,280 15,280 Melanoma 59,940 33,91026,030 8,110 5,220 2,890

There thus remains a need for new efficacious and safe treatment optionfor glioblastoma, prostate tumor, breast cancer, esophageal cancer,colorectal cancer, clear cell renal cell carcinoma, lung cancer, CNS,ovarian, melanoma (Tamm et al. 1998) pancreatic cancer, squamous cellcarcinoma, leukemia and medulloblastoma and other tumors that show anoverexpression of survivin, as well as enhancing the well-being of thepatients without using chemotherapeutic agents or other agents which maylead to severe side effects.

SUMMARY OF THE INVENTION

In a first aspect thereof, the present invention relates to a peptidecomprising a sequence selected from the group of SEQ ID NO: 1 to SEQ IDNO: 3, or a variant thereof that is at least 85% homologous to SEQ IDNO: 1 to SEQ ID NO: 3, or a variant thereof that induces T cellscross-reacting with said variant peptide; wherein said peptide is notthe full-length polypeptide of human survivin. Preferably, said peptideis selected from a peptide having a specific HLA-subtype, such asHLA-A*02 or HLA-DR.

In a second aspect thereof, the present invention relates to a nucleicacid, encoding a peptide according to the present invention or anexpression vector capable of expressing said nucleic acid.

In a third aspect thereof, the present invention relates to a host cellcomprising the nucleic acid or the expression vector according to thepresent invention, wherein the host cell preferably is an antigenpresenting cell, in particular a dendritic cell or antigen presentingcell.

In a fourth aspect, the present invention relates to an in vitro methodfor producing activated cytotoxic T lymphocytes (CTL), comprisingcontacting in vitro CTL with antigen loaded human class I MHC moleculesexpressed on the surface of a suitable antigen-presenting cell or anartificial construct mimicking an antigen-presenting cell for a periodof time sufficient to activate the CTL in an antigen specific manner,wherein the antigen is a peptide according to the present invention.

The present invention also provides a use of a peptide, the nucleicacid, the expression vector, the host cell, or an activated cytotoxic Tlymphocyte produced according to the present invention for the treatmentof cancer or for the manufacture of a medicament against cancer. Themedicament is preferably a vaccine. Preferably, the cancer is selectedfrom astrocytoma, pilocytic astrocytoma, dysembryoplasticneuroepithelial tumor, oligodendrogliomas, ependymoma, glioblastomamultiforme, mixed gliomas, oligoastrocytomas, medulloblastoma,retinoblastoma, neuroblastoma, germinoma, teratoma, gangliogliomas,gangliocytoma, central gangliocytoma, primitive neuroectodermal tumors(PNET, e.g. medulloblastoma, medulloepithelioma, neuroblastoma,retinoblastoma, ependymoblastoma), tumors of the pineal parenchyma (e.g.pineocytoma, pineoblastoma), ependymal cell tumors, choroid plexustumors, neuroepithelial tumors of uncertain origin (e.g. gliomatosiscerebri, astroblastoma), glioblastoma prostate tumor, breast cancer,esophageal cancer, colon cancer, colorectal cancer, renal cellcarcinoma, clear cell renal cell carcinoma, lung cancer, CNS, ovarian,melanoma pancreatic cancer, squamous cell carcinoma, leukemia andmedulloblastoma, and other tumors or cancers showing an overexpressionof Survivin.

The present invention also provides a kit, comprising: (a) a containerthat contains a pharmaceutical composition containing a peptide, a thenucleic acid or the expression vector according to a host cell, or anactivated cytotoxic T lymphocyte according to the present invention, insolution or in lyophilized form; (b) optionally, a second containercontaining a diluent or reconstituting solution for the lyophilizedformulation; (c) optionally, at least one peptide selected from thegroup consisting of the peptides according to SEQ ID NOS: 4 to 24, and(d) optionally, instructions for the use of the solution and/or thereconstitution and/or use of the lyophilized formulation.

The present invention also provides a method for producing a recombinantantibody that specifically binds to a human major histocompatibilitycomplex (MEC) class I or II complexed with a HLA-restricted antigen. Themethod comprises immunizing a genetically engineered non-human mammalhaving cells that expresses a human major histocompatibility complex(MEC) class I or II. The non-human mammal is immunized with a solubleform of a MHC class I or II molecule complexed with a HLA-restrictedantigen. mRNA molecules are isolated from antibody producing cells ofthe non-human mammal. A phage display library displaying proteinmolecules encoded by the mRNA molecules is provided. At least one phageis isolated from the phage display library, wherein the at least onephage displaying the antibody specifically binds to the human majorhistocompatibility complex (MEC) class I or II complexed with theHLA-restricted antigen.

The present invention further provides an antibody that specificallybinds to a human major histocompatibility complex (MHC) class I or IIcomplexed with a HLA-restricted antigen, wherein the antibody ispreferably is a polyclonal antibody, monoclonal antibody and/or achimeric antibody.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the ESI-liquid chromatography mass spectrum identifying thetumor associated peptide NCAN-001 from the glioblastoma sample GB1006.

FIG. 2 depicts the mRNA expression profile of the gene NCAN encoding theglioblastoma associated peptide NCAN-001. Expression of this gene isabsent or very low in normal tissues while it is strongly increased inglioblastoma samples (GB1006T to GB1011T; NCH359T and NCH361T).

FIG. 3 depicts the relative mRNA expression profile of the gene BIRC.5Expression of this gene is absent or very low in normal tissues while itis strongly increased in tumor samples.

FIGS. 4a and 4b depict the presence of PSMA and Survivin-specificIFNγ-secreting CD4⁺T-cells in peripheral blood mononuclear cells (PBMC)from different time points of a vaccinated patient which were determinedusing an IFNγ-ELISPOT®. Time points: pre-vaccination (a) and after3.(b), 6.(c), 7.(d), 8.(e), 9.(f), 10.(g), 11.(h) vaccination.

FIG. 5 shows the presence of Survivin-specific IFNγ-, IL-5, IL-10,TNFα-secreting CD4⁺T-cells in PBMC from three different time points of avaccinated patient that were determined via ICS-Assay. Time points:after 1.(a), 3.(b), 7.(c), vaccination.

FIG. 6 shows the biochemical response in patients 8 and 10, showing PSAstability with no rise greater than 10% from baseline PSA.

FIG. 7 shows the biochemical response in patients 11 and 16, showing PSADT increase without PSA stability.

FIG. 8 shows the biochemical response in patient 5, showing PSA DTincrease without PSA stability.

FIG. 9 shows the biochemical response in patients 1, 4, 10, 12 and 13showing no change of PSA DT during vaccination.

FIG. 10 shows the biochemical response in patients 2, 6, 9, 14, 18 and19 showing no change of PSA DT during vaccination.

FIG. 11 shows the biochemical response in patients 7, 15 and 17 showinginterim PSA decline or DT increase followed by DT decrease.

FIG. 12 shows that from the prostate cancer vaccination study,BIR-002-peptide-specific CD4+ T-cell clones could be established fromseveral vaccinated cancer patients that are functional with respect toIFN-gamma production in response to BIR-002. Wang et al., 2008 describeT-cell clones obtained from healthy donors only after several rounds ofin vitro priming and stimulation, while the present T-cells can beinduced in patients by vaccinations. PMA/ionomycin=antigen-independentunspecific activation; Survivin (II): BIR-002 stimulation; PSMA (II):stimulation with irrelevant peptide. All reactive cells are CD4positive.

FIG. 13 shows that BIR-002 is naturally presented by dendritic cells.Immature dendritic cells incubated with recombinant survivin protein arerecognized by BIR-002 specific T-cells from vaccinated patients as shownby intracellular cytokine staining. These results suggest that BIR-002is naturally processed by proteinases within dendritic cells and thatthe BIR-002 epitope is not destroyed by processing. In addition, theseCD4+ T-cells are multifunctional as they secrete cytokines IFN-gamma,TNF-alpha and IL-2, have surface expression of CD40 ligand (CD154) anddegranulate indicated by surface expression of CD 107a. The indicatedT-cell response is antigen-specific, as the T-cells are not activated bydendritic cells incubated with the irrelevant protein RAP80, or HIV-001peptide.

FIG. 14 shows that a high fraction of BIR-002-specific CD4+ T cellsderived from BIR-002 vaccinated prostate cancer patients expressbeneficial cytokines IFN-gamma, TNF-alpha, IL-2 while theimmunoregulatory cytokines IL-10 and IL-17 are not expressed to thatextent. Shown are primary data and summarized data from intracellularcytokine staining of T-cells specific for BIR-002 or two control classII restricted peptides.

FIG. 15 shows that several tumor cell lines expressing different HLA-DRalleles are recognized by patient-derived PBMCs (shown for the patientsPro26 and Pro15). Patients develop multi-clonal T-cell responses aftervaccination with BIR-002. BIR-002 shows promiscuous binding to severalHLA class II alleles: DR1; (see also Wang et al.); DQ5 (not tested byWang et al.); DR11 (see also Wang et al.); or DRB3 (in contrast to Wanget al., 2008, Table 1). Functional presentation of BIR-002 is possiblein the context of several HLA class II molecules (TNF-alpha production).As for HLA class I (HLA-A, -B, C), in principle, also three differentgene loci can be found for HLA class II that express functional class IImolecules on the cell surface, namely HLA-DQ, HLA-DP and HLA-DR. Class Imolecules are composed of a heavy chain (-A, -B, -C) and abeta-2-microglobulin that is constant in all three genes. Nevertheless,class II molecules are composed of two each of variable chains (alphaand beta). Thus, sophisticated genetically typing is always complicatedwith class II. In the table so-called serologic types are given, whichare based on antibody binding. Thus, “DQ3” for example comprisesdifferent alleles of HLA-DQ alpha and beta chains that are commonlyfound together and react with a particular antibody. The cells in thetable are:

important prerequisite for the natural presentation of “genuine” T cellepitopes from an intracellular processing of the protein antigen. Themeasured half-maximal proliferative activity of the peptide-specific Tcell clones were <50 nM for Sio, 400-700 nM for S40, 2000-3000 nM forS88 and 100-300 nM for P58. Piesche further disclosed that only the SVNpeptide S10 elided elicited a specific T cell proliferation duringexposure with recombinant SVN protein. This was shown in threeSio-specific T cell clones from different donors. Piesche et al.investigated the processing and presentation of SVN peptide epitopesfrom natural antigen by co-culturing of peptide-specific T cell cloneswith SVN protein-pulsed DCs. Only the SVN peptide S₁₀ was able to causespecific T cell proliferation during exposure with recombinant SVNprotein. This was shown in three Sio-specific T cell clones fromdifferent donors. No specific proliferation in response to the naturalantigen was detected for the PR₃-specific T cell clones.

Name cell line Reference AL E418 EBV Human Immunology Volume 51,transformed B-cell line Issue 1, November 1996, Pages 13-22 LAM Blymphoma cell line Oncogenomics 19 Sep. 2002, Volume 21, Number 42,Pages 6549-6556 HO301 EBV transformed B The Journal of Immunology, 1998,cell line 160: 3363-3373. BM15 Dr11 + APC cell line The Journal ofImmunology, 2004, 173: 1876-1886 MGAR homozygous B-LCL Gene Therapy(2004) 11, 1408-1415 LG2-EBV autologous B cell line Cancer Immunity,Vol. 2, p. 9 (19 Jul. 2002) EMJ B Lymphoblastoid ECACC NO: 8602103 IHWNumber Cell Line 9097: and Hum Immunol. 1980 December; 1(4): 363-8.

DETAILED DESCRIPTION OF THE INVENTION

The term “peptide” is used herein to designate a series of amino acidresidues, connected one to the other typically by peptide bonds betweenthe alpha-amino and carbonyl groups of the adjacent amino acids. Thepeptides are typically 9 amino acids in length, but can be as short as 8amino acids in length, and as long as 16 amino acids in length.

The term “oligopeptide” is used herein to designate a series of aminoacid residues, connected one to the other typically by peptide bondsbetween the alpha-amino and carbonyl groups of the adjacent amino acids.The length of the oligopeptide is not critical to the invention, as longas the correct epitope or epitopes are maintained therein. Theoligopeptides are typically less than about 30 amino acid residues inlength, and greater than about 14 amino acids in length.

The term “polypeptide” designates a series of amino acid residues,connected one to the other typically by peptide bonds between thealpha-amino and carbonyl groups of the adjacent amino acids. The lengthof the polypeptide is not critical to the invention as long as thecorrect epitopes are maintained. In contrast to the terms peptide oroligopeptide, the term polypeptide is meant to refer to moleculescontaining more than about 30 amino acid residues.

A peptide, oligopeptide, protein, or polynucleotide coding for such amolecule is “immunogenic” (and thus an “immunogen” within the presentinvention), if it is capable of inducing an immune response. In the caseof the present invention, immunogenicity is more specifically defined asthe ability to induce a T-cell response. Thus, an “immunogen” would be amolecule that is capable of inducing an immune response, and in the caseof the present invention, a molecule capable of inducing a T-cellresponse.

A T cell “epitope” requires a short peptide that is bound to a class Ior II MHC receptor, which forms a ternary complex (MHC class I alphachain, beta-2-microglobulin, and peptide) that can be recognized by a Tcell bearing a matching T-cell receptor binding to the MHC/peptidecomplex with appropriate affinity. Peptides binding to MHC class Imolecules are typically 8 to 14 amino acids in length, and mosttypically 9 amino acids in length. T cell epitopes that bind to MHCclass II molecules are typically 12 to 30 amino acids in length. In thecase of peptides that bind to MHC class II molecules, the same peptideand the corresponding T cell epitope may share a common core segment,but differ in the overall length due to flanking sequences of differinglengths upstream of the amino-terminus of the core sequence anddownstream of its carboxy-terminus, respectively. MHC class II receptorshave a more open conformation, peptides bound to MHC class II receptorsare correspondingly not completely buried in the structure of the MHCclass II molecule peptide-binding cleft as they are in the MHC class Imolecule peptide-binding cleft. Surprisingly, this is not the case forthe peptide according to SEQ ID NO: 1, as small variations in the lengthof the peptide lead to an extreme decrease of activity (see below).

In humans there are three different genetic loci that encode MHC class Imolecules (the MHC-molecules of the human are also designated humanleukocyte antigens (HLA)): HLA-A, HLA-B, and HLA-C. HLA-A*01, HLA-A*02,and HLA-A*11 are examples of different MHC class I alleles that can beexpressed from these loci.

TABLE 2 Top 30 expressed alleles in different populations % chance ofallele expressed in an individual Top 30 expressed alleles AlleleCaucasian Allele African-American Allele Hispanic Allele Asian A*020145.6% C*0401 29.0% A*0201 37.1% A*1101 38.4% C*0701 27.7% C*0701 25.4%C*0401 25.4% A*2402 33.7% A*0101 27.4% C*0602 23.0% A*2402 24.9% C*070233.3% A*0301 23.8% A*0201 22.3% C*0702 24.2% C*0102 27.7% C*0702 21.5%A*2301 20.7% C*0701 20.8% A*3303 23.3% C*0401 21.2% C*0202 19.0% C*030414.4% C*0801 21.6% B*4402 20.2% A*0301 18.7% A*0301 14.3% C*0304 19.9%B*0702 18.1% C*0702 18.1% B*0702 13.2% A*0201 18.1% B*0801 18.1% B*530118.1% B*3501 12.8% B*4001 15.2% C*0501 17.2% B*0702 15.8% C*0602 12.3%C*0401 14.0% C*0304 16.8% C*1601 15.7% C*0501 11.9% B*5801 13.3% C*060215.7% B*1503 13.9% A*0101 11.4% B*4601 12.7% A*1101 15.3% B*5801 13.5%A*1101 11.0% B*5101 12.4% B*4001 13.6% A*6802 12.7% B*5101 10.8% C*030212.0% A*2402 12.1% C*1701 11.7% C*1601 10.6% B*3802 11.4% B*3501 10.7%B*4501 10.8% B*4403 9.9% A*0207 11.0% C*0303 10.6% B*4201 10.5% C*01029.7% B*1501 9.4% B*5101 10.4% A*3001 10.4% A*2902 9.7% A*0206 9.3%C*1203 9.9% B*3501 10.1% C*0802 9.3% C*0303 9.2% B*1501 9.6% A*010110.0% B*1801 9.1% B*1502 9.1% A*2902 8.9% C*0304 9.3% A*3101 8.9% A*02038.8% A*2601 8.2% A*3002 9.2% B*5201 8.6% B*4403 8.6% A*3201 8.2% B*08018.5% B*1402 8.6% C*1402 8.4% C*0802 7.7% A*3402 8.4% C*0202 7.6% B*35017.2% A*2501 7.5% A*7401 8.4% C*1203 7.6% C*0602 7.0% B*5701 7.1% A*33038.0% A*2601 7.6% B*5401 6.9% B*1402 6.7% C*1801 7.3% A*6801 7.1% B*13016.6% C*0202 6.6% A*2902 7.2% B*0801 7.0% B*4002 6.3% B*1801 6.4% B*44036.9% A*3002 6.8% B*5502 6.3% B*4403 6.4% B*4901 6.9% B*4402 6.5% A*26016.0%

There are 3 different loci in the human genome for MHC class II genes:HLA-DR, HLA-DQ, and HLA-DP. MHC class II receptors are heterodimersconsisting of an alpha and a beta chain, both anchoring in the cellmembrane via a transmembrane region. HLA-DRB1*04, and HLA-DRB1*07 aretwo examples of different MHC class II beta alleles that are known to beencoded in these loci. Class II alleles are very polymorphic, e.g.several hundred different HLA-DRB1 alleles have been described.Therefore, for therapeutic and diagnostic purposes a peptide that bindswith appropriate affinity to several different HLA class II receptors ishighly desirable. A peptide binding to several different HLA class IImolecules is called a promiscuous binder.

As used herein, reference to a DNA sequence includes both singlestranded and double stranded DNA. Thus, the specific sequence, unlessthe context indicates otherwise, refers to the single strand DNA of suchsequence, the duplex of such sequence with its complement (doublestranded DNA) and the complement of such sequence. The term “codingregion” refers to that portion of a gene that either naturally ornormally codes for the expression product of that gene in its naturalgenomic environment, i.e., the region coding in vivo for the nativeexpression product of the gene.

The coding region can be from a normal, mutated or altered gene, or caneven be from a DNA sequence, or gene, wholly synthesized in thelaboratory using methods well known to those of skill in the art of DNAsynthesis.

The term “nucleotide sequence” refers to a heteropolymer ofdeoxyribonucleotides.

The nucleotide sequence coding for a particular peptide, oligopeptide,or polypeptide may be naturally occurring or may be syntheticallyconstructed. Generally, DNA segments encoding the peptides,polypeptides, and proteins of this invention are assembled from cDNAfragments and short oligonucleotide linkers, or from a series ofoligonucleotides, to provide a synthetic gene that is capable of beingexpressed in a recombinant transcriptional unit comprising regulatoryelements preferably derived from a microbial or viral operon.

The term “expression product” means the polypeptide or protein that isthe natural translation product of the gene and any nucleic acidsequence coding equivalents resulting from genetic code degeneracy andthus coding for the same amino acid(s).

The term “fragment,” when referring to a coding sequence, means aportion of DNA comprising less than the complete coding region, whoseexpression product retains essentially the same biological function oractivity as the expression product of the complete coding region.

The term “DNA segment” refers to a DNA polymer, in the form of aseparate fragment or as a component of a larger DNA construct, which hasbeen derived from DNA isolated at least once in substantially pure form,i.e., free of contaminating endogenous materials and in a quantity orconcentration enabling identification, manipulation, and recovery of thesegment and its component nucleotide sequences by standard biochemicalmethods, for example, by using a cloning vector. Such segments areprovided in the form of an open reading frame uninterrupted by internalnontranslated sequences, or introns, which are typically present ineukaryotic genes. Sequences of non-translated DNA may be presentdownstream from the open reading frame, where the same do not interferewith manipulation or expression of the coding regions.

The term “primer” means a short nucleic acid sequence that can be pairedwith one strand of DNA and provides a free 3′-OH end at which a DNApolymerase can start synthesis of a deoxyribonucleotide chain.

The term “promoter” means a region of DNA involved in binding of RNApolymerase to initiate transcription.

The term “open reading frame (ORF)” means a series of triplets codingfor amino acids without any termination codons and is a sequence(potentially) translatable into protein.

The term “isolated” means that the material is removed from its originalenvironment (e.g., the natural environment if it is naturallyoccurring). For example, a naturally-occurring polynucleotide orpolypeptide present in a living animal is not isolated, but the samepolynucleotide or polypeptide, separated from some or all of thecoexisting materials in the natural system, is isolated. Suchpolynucleotides could be part of a vector and/or such polynucleotides orpolypeptides could be part of a composition, and still be isolated inthat such vector or composition is not part of its natural environment.

The polynucleotides, and recombinant or immunogenic polypeptides,disclosed in accordance with the present invention may also be in“purified” form. The term “purified” does not require absolute purity;rather, it is intended as a relative definition, and can includepreparations that are highly purified or preparations that are onlypartially purified, as those terms are understood by those of skill inthe relevant art. For example, individual clones isolated from a cDNAlibrary have been conventionally purified to electrophoretichomogeneity. Purification of starting material or natural material to atleast one order of magnitude, preferably two or three orders, and morepreferably four or five orders of magnitude is expressly contemplated.Furthermore, the claimed polypeptide which has a purity of preferably99.999%, or at least 99.99% or 99.9%; and even desirably 99% by weightor greater is expressly contemplated.

The nucleic acids and polypeptide expression products disclosedaccording to the present invention, as well as expression vectorscontaining such nucleic acids and/or such polypeptides, may be in“enriched form.” As used herein, the term “enriched” means that theconcentration of the material is at least about 2, 5, 10, 100, or 1000times its natural concentration (for example), advantageously 0.01%, byweight, preferably at least about 0.1% by weight. Enriched preparationsof about 0.5%, 1%, 5%, 10%, and 20% by weight are also contemplated. Thesequences, constructs, vectors, clones, and other materials comprisingthe present invention can advantageously be in enriched or isolatedform.

The term “active fragment” means a fragment that generates an immuneresponse (i.e., has immunogenic activity) when administered, alone oroptionally with a suitable adjuvant, to an animal, such as a mammal, forexample, a rabbit or a mouse, and also including a human, such immuneresponse taking the form of stimulating a T-cell response within therecipient animal, such as a human. Alternatively, the “active fragment”may also be used to induce a T-cell response in vitro.

As used herein, the terms “portion,” “segment,” and “fragment,” whenused in relation to polypeptides, refer to a continuous sequence ofresidues, such as amino acid residues, which sequence forms a subset ofa larger sequence. For example, if a polypeptide were subjected totreatment with any of the common endopeptidases, such as trypsin orchymotrypsin, the oligopeptides resulting from such treatment wouldrepresent portions, segments or fragments of the starting polypeptide.This means that any such fragment will necessarily contain as part ofits amino acid sequence a segment, fragment or portion, that issubstantially identical, if not exactly identical, to a sequence of SEQID NO: 1 to SEQ ID NO: 3, which correspond to the naturally occurring,or “parent” protein of the SEQ ID NO: 1 to SEQ ID NO: 3, namelysurvivin. When used in relation to polynucleotides, such terms refer tothe products produced by treatment of said polynucleotides with any ofthe common endonucleases.

In accordance with the present invention, the term “percent identity” or“percent identical,” when referring to a sequence, means that a sequenceis compared to a claimed or described sequence after alignment of thesequence to be compared (the “Compared Sequence”) with the described orclaimed sequence (the “Reference Sequence”). The Percent Identity isthen determined according to the following formula:Percent Identity=100[I−(C/R)]

wherein C is the number of differences between the Reference Sequenceand the Compared Sequence over the length of alignment between theReference Sequence and the Compared Sequence, wherein

(i) each base or amino acid in the Reference Sequence that does not havea corresponding aligned base or amino acid in the Compared Sequence and

(ii) each gap in the Reference Sequence and

(iii) each aligned base or amino acid in the Reference Sequence that isdifferent from an aligned base or amino acid in the Compared Sequence,constitutes a difference;

and R is the number of bases or amino acids in the Reference Sequenceover the length of the alignment with the Compared Sequence with any gapcreated in the Reference Sequence also being counted as a base or aminoacid.

If an alignment exists between the Compared Sequence and the ReferenceSequence for which the percent identity as calculated above is aboutequal to or greater than a specified minimum Percent Identity, then theCompared Sequence has the specified minimum percent identity to theReference Sequence even though alignments may exist in which the hereinabove calculated Percent Identity is less than the specified PercentIdentity.

The original peptides disclosed herein can be modified by thesubstitution of one or more residues at different, possibly selective,sites within the peptide chain, if not otherwise stated. Suchsubstitutions may be of a conservative nature, for example, where oneamino acid is replaced by an amino acid of similar structure andcharacteristics, such as where a hydrophobic amino acid is replaced byanother hydrophobic amino acid. Even more conservative would bereplacement of amino acids of the same or similar size and chemicalnature, such as where leucine is replaced by isoleucine. In studies ofsequence variations in families of naturally occurring homologousproteins, certain amino acid substitutions are more often tolerated thanothers, and these are often show correlation with similarities in size,charge, polarity, and hydrophobicity between the original amino acid andits replacement, and such is the basis for defining “conservativesubstitutions.”

Conservative substitutions are herein defined as exchanges within one ofthe following five groups: Group 1—small aliphatic, nonpolar or slightlypolar residues (Ala, Ser, Thr, Pro, Gly); Group 2—polar, negativelycharged residues and their amides (Asp, Asn, Glu, Gln); Group 3—polar,positively charged residues (His, Arg, Lys); Group 4—large, aliphatic,nonpolar residues (Met, Leu, Ile, Val, Cys); and Group 5—large, aromaticresidues (Phe, Tyr, Trp).

Less conservative substitutions might involve the replacement of oneamino acid by another that has similar characteristics but is somewhatdifferent in size, such as replacement of an alanine by an isoleucineresidue. Highly non-conservative replacements might involve substitutingan acidic amino acid for one that is polar, or even for one that isbasic in character. Such “radical” substitutions cannot, however, bedismissed as potentially ineffective since chemical effects are nottotally predictable and radical substitutions might well give rise toserendipitous effects not otherwise predictable from simple chemicalprinciples.

Of course, such substitutions may involve structures other than thecommon L-amino acids. Thus, D-amino acids might be substituted for theL-amino acids commonly found in the antigenic peptides of the inventionand yet still be encompassed by the disclosure herein. In addition,amino acids possessing non-standard R groups (i.e., R groups other thanthose found in the common 20 amino acids of natural proteins) may alsobe used for substitution purposes to produce immunogens and immunogenicpolypeptides according to the present invention.

If substitutions at more than one position are found to result in apeptide with substantially equivalent or greater antigenic activity asdefined below, then combinations of those substitutions will be testedto determine if the combined substitutions result in additive orsynergistic effects on the antigenicity of the peptide. At most, no morethan four positions within the peptide would simultaneously besubstituted.

The term “T-cell response” means the specific proliferation andactivation of effector functions induced by a peptide in vitro or invivo. For MHC class I restricted CTLs, effector functions may be lysisof peptide-pulsed, peptide-precursor pulsed or naturallypeptide-presenting target cells, secretion of cytokines, preferablyInterferon-gamma, TNF-alpha, or IL-2 induced by peptide, secretion ofeffector molecules, preferably granzymes or perforins induced bypeptide, or degranulation. For MHC class II-restricted T helper cells,effector functions may be peptide induced secretion of cytokines,preferably, IFN-gamma, TNF-alpha, IL-4, IL-5, IL-10, or IL-2, orpeptide-induced degranulation. Possible effector functions for CTLs andT helper cells are not limited to this list.

Preferably, when the CTLs specific for a peptide derived from any of SEQID NO: 1 to 3 are tested against the substituted peptides, the peptideconcentration at which the substituted peptides achieve half the maximalincrease in lysis relative to background is no more than about 1 mM,preferably no more than about 1 μM, more preferably no more than about 1nM, and still more preferably no more than about 100 μM, and mostpreferably no more than about 10 μM. It is also preferred that thesubstituted peptide be recognized by CTLs from more than one individual,at least two, and more preferably three individuals.

Thus, the epitopes of the present invention may be identical tonaturally occurring tumor-associated or tumor-specific epitopes or mayinclude epitopes that differ by no more than four residues from thereference peptide, as long as they have substantially identicalantigenic activity.

Stimulation of an immune response is dependent upon the presence ofantigens recognized as foreign by the host immune system. The discoveryof the existence of tumor associated antigens has now raised thepossibility of using a host's immune system to foster an immune responsethat is specific for target antigens expressed on the surface of tumorcells and which through this mechanism of action is capable of inducingregression, stasis or slowed-down growth of the tumor. Variousmechanisms of harnessing both the humoral and cellular arms of theimmune system are currently being explored for cancer immunotherapy.

Specific elements of the cellular immune response are capable ofspecifically recognizing and destroying tumor cells. The isolation ofcytotoxic T cells (CTL) from tumor-infiltrating cell populations or fromperipheral blood suggests that such cells play an important role innatural immune defenses against cancer (Cheever et al., 1993; Zeh, IIIet al., 1999). Based on the analysis of 415 specimens from patientssuffering from colorectal cancer, Galon et al. were able to demonstratethat type, density and location of immune cells in tumor tissue areactually a better predictor for survival of patients than the widelyemployed TNM-staging of tumors (Galon et al., 2006).

MHC class I present peptides that result from proteolytic cleavage ofpredominantly endogenous proteins, DRIPs and larger peptides. MHC classII molecules can be found predominantly on professional antigenpresenting cells (APCs), and primarily present peptides of exogenous ortransmembrane proteins that are taken up by APCs during the course ofendocytosis, and are subsequently processed (Cresswell, 1994). Complexesof peptide and MHC class I molecules are recognized by CD8-positivecytotoxic T-lymphocytes bearing the appropriate TCR (T-cell receptor),and complexes of peptide and MHC class II molecules are recognized byCD4-positive-helper-T cells bearing the appropriate TCR. It is wellknown that the TCR, the peptide and the MHC are thereby present in astoichiometric amount of 1:1:1.

CD4-positive helper T cells play an important role in inducing andsustaining effective responses by CD8-positive cytotoxic T cells (Wangand Livingstone, 2003; Sun and Bevan, 2003; Shedlock and Shen, 2003).Initially, the priming and expansion of CTLs in lymph nodes is supportedby CD4+ T-cells (Schoenberger et al., 1998). One mechanism thereforemight be the guidance of naive CD8+ cells to the place of functionalCD4+ T-cell—APC interaction (Castellino et al., 2006). Finally, thegeneration of functional CD8+ memory cells is in most cases dependent onCD4+ T-cell assistance (Sun and Bevan, 2003; Janssen et al., 2003). Forthese reasons, the identification of CD4-positive T-cell epitopesderived from tumor associated antigens (TAA) is of great importance forthe development of pharmaceutical products for triggering anti-tumorimmune responses (Kobayashi et al., 2002; Qin et al., 2003; Gnjatic etal., 2003). At the tumor site, T helper cells, support a CTL friendlycytokine milieu (Qin and Blankenstein, 2000; Mortara et al., 2006) andattract effector cells, e.g. CTLS, NK cells, macrophages, granulocytes(Marzo et al., 2000; Hwang et al., 2007).

In the absence of inflammation, expression of MHC class II molecules ismainly restricted to cells of the immune system, especially professionalantigen-presenting cells (APC), e.g., monocytes, monocyte-derived cells,macrophages, and dendritic cells. In cancer patients, cells of the tumorhave surprisingly been found to express MHC class II molecules (Dengjelet al., 2006).

It was shown in mammalian animal models, e.g., mice, that even in theabsence of CTL effector cells (i.e., CD8-positive T lymphocytes),CD4-positive T cells are sufficient for inhibiting manifestation oftumors via inhibition of angiogenesis by secretion of interferon-gamma(IFNγ) (Qin and Blankenstein, 2000). Also the direct killing of tumorcells by cytotoxic CD4+ T cells via lymphotoxins and granzyme B has beenproposed (Penna et al., 1992; Littaua et al., 1992).

Additionally, it was shown that CD4-positive T cells recognizingpeptides from tumor-associated antigens presented by HLA class IImolecules can counteract tumor progression via the induction of antibody(Ab) responses (Kennedy et al., 2003).

In contrast to tumor-associated peptides binding to HLA class Imolecules, only a small number of class II ligands of tumor associatedantigens (TAA) have been described to date.

Since the constitutive expression of HLA class II molecules is usuallylimited to cells of the immune system (Mach et al., 1996), thepossibility of isolating class II peptides directly from primary tumorswas not considered possible. However, Dengjel et al. were recentlysuccessful in identifying a number of MHC Class II epitopes directlyfrom tumors (WO 2007/028574, EP 1 760 088 B1; (Dengjel et al., 2006).

The antigens that are recognized by the tumor specific cytotoxic Tlymphocytes, that is, their epitopes, can be molecules derived from allprotein classes, such as enzymes, receptors, transcription factors, etc.which are expressed and, as compared to unaltered cells of the sameorigin, up-regulated in cells of the respective tumor.

The current classification of tumor associated antigens (TAAs) comprisesthe following major groups (Novellino et al., 2005):

1. Cancer-testis antigens: The first TAAs ever identified that can berecognized by T cells (van der Bruggen et al., 1991) belong to thisclass, which was originally called cancer-testis (CT) antigens becauseof the expression of its members in histologically different humantumors and, among normal tissues, only in spermatocytes/spermatogonia oftestis and, occasionally, in placenta. Since the cells of testis do notexpress class I and II HLA molecules, these antigens cannot berecognized by T cells in normal tissues and can therefore be consideredas immunologically tumor-specific. Well-known examples for CT antigensare the MAGE family members or NY-ESO-1.

2. Differentiation antigens: These TAAs are shared between tumors andthe normal tissue from which the tumor arose; most are found inmelanomas and normal melanocytes. Many of these melanocytelineage-related proteins are involved in the biosynthesis of melanin andare therefore not tumor specific, but nevertheless are widely used forcancer immunotherapy. Examples include, but are not limited to,tyrosinase and Melan-A/MART-1 for melanoma or PSA for prostate cancer.

3. Overexpressed TAAs: Genes encoding widely expressed TAAs have beendetected in histologically different types of tumors as well as in manynormal tissues, generally with lower expression levels. It is possiblethat many of the epitopes processed and potentially presented by normaltissues are below the threshold level for T-cell recognition, whiletheir overexpression in tumor cells can trigger an anticancer responseby breaking previously established tolerance. Prominent examples forthis class of TAAs are Her-2/neu, Survivin, Telomerase or WT1.

4. Tumor specific antigens: These unique TAAs arise from mutations ofnormal genes (such as β-catenin, CDK4, etc.). Some of these molecularchanges are associated with neoplastic transformation and/orprogression. Tumor specific antigens are generally able to induce strongimmune responses without bearing the risk for autoimmune reactionsagainst normal tissues. On the other hand, these TAAs are in most casesonly relevant to the exact tumor on which they were identified and areusually not shared between many individual tumors.

5. TAAs arising from abnormal post-translational modifications: SuchTAAs may arise from proteins that are neither specific nor overexpressedin tumors but nevertheless become tumor associated by posttranslationalprocesses primarily active in tumors. Examples for this class arise fromaltered glycosylation patterns leading to novel epitopes in tumors asfor MUC1 or events like protein splicing during degradation, which mayor may not be tumor specific (Hanada et al., 2004; Vigneron et al.,2004).

6. Oncoviral proteins: These TAAs are viral proteins that may play acritical role in the oncogenic process and, because they are foreign(not of human origin), they can evoke a T-cell response. Examples ofsuch proteins are the human papilloma type 16 virus proteins, E6 and E7,which are expressed in cervical carcinoma.

For proteins to be recognized by cytotoxic T-lymphocytes astumor-specific or -associated antigens, and to be used in a therapy,particular prerequisites must be fulfilled. The antigen should beexpressed mainly by tumor cells and not or in comparably small amountsby normal healthy tissues. It is furthermore desirable, that therespective antigen is not only present in a type of tumor, but also inhigh concentrations (i.e. copy numbers of the respective peptide percell). Tumor-specific and tumor-associated antigens are often derivedfrom proteins directly involved in transformation of a normal cell to atumor cell due to a function e.g. in cell cycle control or suppressionof apoptosis. Additionally, also downstream targets of the proteinsdirectly causative for a transformation may be upregulated and thus maybe indirectly tumor-associated. Such indirectly tumor-associatedantigens may also be targets of a vaccination approach (Singh-Jasuja etal., 2004). In both cases it is essential that epitopes are present inthe amino acid sequence of the antigen, since such a peptide(“immunogenic peptide”) that is derived from a tumor associated antigenshould lead to an in vitro or in vivo T-cell-response.

Basically, any peptide able to bind a MHC molecule may function as aT-cell epitope. A prerequisite for the induction of an in vitro or invivo T-cell-response is the presence of a T cell with a correspondingTCR and the absence of immunological tolerance for this particularepitope.

Therefore, TAAs are a starting point for the development of a tumorvaccine. The methods for identifying and characterizing the TAAs arebased on the use of CTL that can be isolated from patients or healthysubjects, or they are based on the generation of differentialtranscription profiles or differential peptide expression patternsbetween tumors and normal tissues (Lemmel et al., 2004; Weinschenk etal., 2002).

However, the identification of genes over-expressed in tumor tissues orhuman tumor cell lines, or selectively expressed in such tissues or celllines, does not provide precise information as to the use of theantigens being transcribed from these genes in an immune therapy. Thisis because only an individual subpopulation of epitopes of theseantigens are suitable for such an application since a T cell with acorresponding TCR has to be present and immunological tolerance for thisparticular epitope needs to be absent or minimal. It is thereforeimportant to select only those peptides from over-expressed orselectively expressed proteins that are presented in connection with MHCmolecules against which a functional T cell can be found. Such afunctional T cell is defined as a T cell that upon stimulation with aspecific antigen can be clonally expanded and is able to executeeffector functions (“effector T cell”).

T-helper cells play an important role in orchestrating the effectorfunction of CTLs in anti-tumor immunity. T-helper cell epitopes thattrigger a T-helper cell response of the T_(H1) type support effectorfunctions of CD8-positive killer T cells, which include cytotoxicfunctions directed against tumor cells displaying tumor-associatedpeptide/MHC complexes on their cell surfaces. In this waytumor-associated T-helper cell peptide epitopes, alone or in combinationwith other tumor-associated peptides, can serve as active pharmaceuticalingredients of vaccine compositions that stimulate anti-tumor immuneresponses.

Since both types of response, CD8 and CD4 dependent, contribute jointlyand synergistically to the anti-tumor effect, the identification andcharacterization of tumor-associated antigens recognized by either CD8+CTLs (ligand: MHC class I molecule+peptide epitope) or by CD4-positiveT-helper cells (ligand: MHC class II molecule+peptide epitope) isimportant in the development of tumor vaccines.

Considering the severe side-effects and expense associated with treatingcancer better prognosis and diagnostic methods are desperately needed.Therefore, there is a need to identify other factors representingbiomarkers for cancer in general and glioblastoma in particular.Furthermore, there is a need to identify factors that can be used in thetreatment of cancer in general and glioblastoma in particular,

Furthermore, there is no established therapeutic design for prostatecancer patients with biochemical relapse after radical prostatectomy,usually caused by residual tumor left in situ in the presence of locallyadvanced tumor growth. New therapeutic approaches that confer lowermorbidity with comparable therapeutic efficacy relative to the currentlyavailable therapeutic approaches would be desirable.

The present invention provides peptides that are useful in treatingglioblastoma, prostate cancer and other tumors that overexpresssurvivin. These peptides were partly directly shown by mass spectrometryto be naturally presented by HLA molecules on primary human glioblastomasamples (see Example 1 and FIG. 1), or in the case of SEQ ID NO: 1 and 2predicted according to the SYFPEITHI prediction algorithm (Rammensee etal., 1995) to be promiscuous binders to the HLA-DR alleles HLA-DRB1*01,DRB1*03, DRB1*04, DRB1*11, and DRB1*15 (see attachment). Based on thisdata and the frequencies of these frequent DRB1 alleles (Mori et al.,1995; Chanock et al., 2004), it can be assumed that 92% of A*02-positiveCaucasians express at least one DRB1 allele that binds these peptides(SEQ ID NO: 1 to SEQ ID NO: 3). SEQ ID NO: 2 contains the same coresequence as SEQ ID NO: 1, elongated by two N-terminal amino acids fromthe natural survivin sequence to contain a described class I T-cellepitope from survivin (Schmitz et al., 2000). SEQ ID NO: 3 contains thesame sequence as SEQ ID NO: 1, wherein the last C-terminal amino acid ismodified from an asparagine (N) to aspartic acid (D).

The source gene from which SEQ ID NO: 1 to SEQ ID NO: 3 arederived—survivin—was shown to be highly overexpressed in glioblastoma,prostate tumor, breast cancer, esophageal cancer, colorectal cancer,clear cell renal cell carcinoma, lung cancer, CNS, ovarian, melanoma(Tamm et al. 1998) pancreatic cancer, squamous cell carcinoma, leukemiaand medulloblastoma compared with normal tissues (see Example 2 and FIG.2) demonstrating a high degree of tumor association of the peptide, i.e.these peptides are strongly presented on tumor tissue but not on normaltissues.

HLA-bound peptides can be recognized by the immune system, specificallyT lymphocytes/T cells. T cells can destroy the cells presenting therecognized HLA/peptide complex, e.g. glioblastoma tumor cells presentingthe survivin-derived (SEQ ID NO: 1 to SEQ ID NO: 3). T helper cellsactivated by the survivin-derived peptides can inhibit tumorvascularization, can attract effector cells of the immune system andfacilitate CTL priming, proliferation, and a sustained CD8+ T-cellresponse.

All peptides of the present invention have been shown to be capable ofstimulating T cell responses (see Example 4 and FIG. 4). Thus, thepeptides are useful for generating an immune response in a patient bywhich tumor cells can be destroyed. An immune response in a patient canbe induced by direct administration of the described peptides orsuitable precursor substances (e.g. elongated peptides, proteins, ornucleic acids encoding these peptides) to the patient, ideally incombination with an agent enhancing the immunogenicity (i.e. anadjuvant). The immune response originating from such a therapeuticvaccination can be expected to be highly specific against tumor cellsbecause the target peptides of the present invention are not presentedon normal tissues in comparable copy numbers, preventing the risk ofundesired autoimmune reactions against normal cells in the patient.

The pharmaceutical compositions comprise the peptides either in the freeform or in the form of a pharmaceutically acceptable salt.

As used herein, “a pharmaceutically acceptable salt” refers to aderivative of the disclosed peptides wherein the peptide is modified bymaking acid or base salts of the agent. For example, acid salts areprepared from the free base (typically wherein the neutral form of thedrug has a neutral —NH₂ group) involving reaction with a suitable acid.Suitable acids for preparing acid salts include both organic acids,e.g., acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalicacid, malic acid, malonic acid, succinic acid, maleic acid, fumaricacid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelicacid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid,salicylic acid, and the like, as well as inorganic acids, e.g.,hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acidphosphoric acid and the like. Conversely, preparation of basic salts ofacid moieties which may be present on a peptide are prepared using apharmaceutically acceptable base such as sodium hydroxide, potassiumhydroxide, ammonium hydroxide, calcium hydroxide, trimethylamine or thelike.

In an especially preferred embodiment the pharmaceutical compositionscomprise the peptides as salts of acetic acid (acetates) or hydrochloricacid (chlorides).

In addition to being useful for treating cancer, the peptides of thepresent invention are also useful as diagnostics. Since the peptideswere generated from glioblastoma and since it was determined that thesepeptides are not present in normal tissues, these peptides can be usedto diagnose the presence of a cancer.

The presence of claimed peptides on tissue biopsies can assist apathologist in diagnosis of cancer. Detection of certain peptides bymeans of antibodies, mass spectrometry or other methods known in the artcan tell the pathologist that the tissue is malignant or inflamed orgenerally diseased. Presence of groups of peptides can enableclassification or subclassification of diseased tissues.

The detection of peptides on diseased tissue specimen can enable thedecision about the benefit of therapies involving the immune system,especially if T lymphocytes are known or expected to be involved in themechanism of action. Loss of MHC expression is a well describedmechanism by which infected of malignant cells escapeimmunosurveillance. Thus, presence of peptides shows that this mechanismis not exploited by the analyzed cells.

The peptides might be used to analyze lymphocyte responses against thosepeptides such as T cell responses or antibody responses against thepeptide or the peptide complexed to MHC molecules. These lymphocyteresponses can be used as prognostic markers for decision on furthertherapy steps. These responses can also be used as surrogate markers inimmunotherapy approaches aiming to induce lymphocyte responses bydifferent means, e.g. vaccination of protein, nucleic acids, autologousmaterials, adoptive transfer of lymphocytes. In gene therapy settings,lymphocyte responses against peptides can be considered in theassessment of side effects. Monitoring of lymphocyte responses mightalso be a valuable tool for follow-up examinations of transplantationtherapies, e.g. for the detection of graft versus host and host versusgraft diseases.

The peptides can be used to generate and develop specific antibodiesagainst MHC/peptide complexes. These can be used for therapy, targetingtoxins or radioactive substances to the diseased tissue. Another use ofthese antibodies can be targeting radionuclides to the diseased tissuefor imaging purposes such as PET. This use can help to detect smallmetastases or to determine the size and precise localization of diseasedtissues.

In addition, they can be used to verify a pathologist's diagnosis of acancer based on a biopsied sample.

Table 3 shows the peptides according to the present invention, theirrespective SEQ ID NO:, the HLA alleles to which the respective peptidesbind, and the source proteins from which these peptides may arise. Ofspecial interest is the fact that the peptide according to SEQ ID NO: 2binds to HLA-DR as well as HLA-A*02, thus eliciting two differentresponses.

TABLE 3 Peptides of the present invention SEQ ID Peptide HLA Source NO:Code Sequence Alleles Protein(s) 1 BIR-002 TLGEFLKLDRERAKN HLA-DRSurvivin 2 BIR-004 ELTLGEFLKLDRERAKN HLA-DR and Survivin HLA-A*02 3BIR-002a TLGEFLKLDRERAKD HLA-DR Survivin

Expression of BIRC5 (survivin), a member of the inhibitor of apoptosisprotein (IAP) family, is elevated in fetal tissues and in various humancancers, with greatly reduced expression in adult normal differentiatedtissues, particularly if their proliferation index is low. Survivinseems to be capable of regulating both cellular proliferation andapoptotic cell death. Although survivin is usually located in the cellcytoplasmic region and associated with poor prognosis in cancer, nuclearlocalization, indicative of favorable prognosis, has also been reported(O'Driscoll et al., 2003). Regulation of and through survivin has beendescribed by several mechanisms. Survivin seems to be associated withthe molecular chaperone Hsp60. In vivo, Hsp60 is abundantly expressed inprimary human tumors as compared with matched normal tissues. Acuteablation of Hsp60 by small interfering RNA destabilizes themitochondrial pool of survivin, induces mitochondrial dysfunction, andactivates caspase-dependent apoptosis (Ghosh et al., 2008). Furthermore,Ras inhibition results in release of the survivin “brake” on apoptosisand in activation of the mitochondrial apoptotic pathway. Especially inglioblastoma, resistance to apoptosis can be abolished by a Rasinhibitor that targets survivin (Blum et al., 2006). There also seems tobe a correlation between NF-kappaB hyperactivity in gliomas andhyperexpression of survivin, one of NF-kappaB target genes. Thus,NF-kappaB-activated anti-apoptotic genes are hyperexpressed in tumorsamples. Especially in glioblastoma, very high levels of survivinexpression are detectable (Angileri et al., 2008). It is suggested thatsurvivin overexpression in brain gliomas might play an important role inmalignant proliferation, anti-apoptosis and angiogenesis (Zhen et al.,2005; Liu et al., 2006). Several analyses were performed to studysurvivin expression and its impact on survival in glioblastoma. Tosummarize, survivin expression, especially the simultaneous expressionin nucleus and cytoplasm in astrocytic tumors was significantlyassociated with malignancy grade (with highest survivin expression inglioblastoma) and shorter overall survival times compared with patientswho had survivin-negative tumors (Kajiwara et al., 2003; Saito et al.,2007; Uematsu et al., 2005; Mellai et al., 2008; Grunda et al., 2006;Xie et al., 2006; Sasaki et al., 2002; Chakravarti et al., 2002).

Survivin-overexpression has also been described for other tumorentities. In breast cancer, survivin expression is associated withhigher grade and shorter disease-free survival (Yamashita et al., 2007;Al-Joudi et al., 2007; Span et al., 2004). In esophageal cancer celllines, the promoter activity of survivin was shown to be 28.5 foldhigher than in normal tissues (Sato et al., 2006). In colorectal cancer,survivin expression is also associated with pathological grade and lymphnode metastasis (Tan et al., 2005). The aggressiveness of clear cellrenal cell carcinoma was shown to be associated with survivinexpression. Furthermore, expression of survivin is inversely associatedwith cancer-specific survival (Kosari et al., 2005). Survivin expressioncan be detected in a panel of keratinocytic neoplasms andhyperproliferative skin lesions but not in normal skin (Bowen et al.,2004). In pancreatic cancer cell lines, survivin was amplified in 58% ofthe tested cell lines (Mahlamaki et al., 2002). In squamous cellcarcinoma, survivin expression can help to identify cases with moreaggressive and invasive clinical phenotype (Lo et al., 2001).

As survivin is such a promising target for cancer therapy, studies usingsurvivin-derived peptides showed that survivin is immunogenic in tumorpatients by eliciting CD8+ T cell-mediated responses. In addition,survivin specifically stimulated CD4+ T-cell reactivity in peripheralblood lymphocytes from the same patients (Casati et al., 2003; Piescheet al., 2007).

Survivin (SVN, BIRO) is overexpressed in a multitude of cancer entities.Thus, in general, overexpression of survivin is thought to be associatedwith shorter overall-survival and higher malignancy grades.

Piesche (2006) disclosed as part of his study (see also (Piesche et al.,2007)), MHC class II and HLA class II-restricted candidate epitopes insurvivin (SVN) and in proteinase-3 (PR3), which were determined usingthe computer program TEPITOPE (Bian and Hammer, 2004). The TEPITOPEanalysis yielded 6 candidate epitopes for SVN and 11 candidate epitopesfor PR3 with high binding probability for various HLA-DR alleles. These17 peptides were used in T cell immunologic experiments after synthesisand chromatographic purification. The variable lengths of the peptidesresulted from overlapping epitopes that were considered together in onepeptide (Table 4).

TABLE 4 Names, AA position, and AA sequences of thesynthetic SVN peptides disclosed by Piesche  2006. Pep- Amino acidT cell tide Position sequence frequency S₁₀ 10-24  WQPFLKDHRISTFKN8.64 * 10⁻⁷ (SEQ ID NO: 28) S₂₂ 22-36  FKNWPFLEGAAATPE  7.2 * 10⁻⁷(SEQ ID NO: 29) S₄₀ 40-54  EAGFIHAPTENEPDL 8.64 * 10⁻⁷ (SEQ ID NO: 30)S₅₈ 58-72  FFCFKELEGWEPDDD 4.32 * 10⁻⁷ (SEQ ID NO: 31) S₈₈ 88-103 LGEFLKLDRERAKNKI 1.73 * 10⁻⁷ (SEQ ID NO: 32) S₁₁₀ 110-124 KNKIAKETNNKKKEF 8.64 * 10⁻⁷ (SEQ ID NO: 33) (Note: S₈₈ actually is S₉₈,thus, Piesche et al. may have made an error in determining the positionof this epitope).

Titration experiments with the corresponding peptides were performed byPiesche to estimate the peptide HLA affinity or the peptide HLA/TCRavidity. The lower the peptide concentration, the higher the bindingaffinity of the peptide epitopes to the MHC molecules, an

important prerequisite for the natural presentation of “genuine” T cellepitopes from an intracellular processing of the protein antigen. Themeasured half-maximal proliferative activity of the peptide-specific Tcell clones were <50 nM for S_(10,), 400-700 nM for S₄₀, 2000-3000 nMfor S₈₈ and 100-300 nM for P₅₈. Piesche further disclosed that only theSVN peptide S10 elicited a specific T cell proliferation during exposurewith recombinant SVN protein. This was shown in three Sio-specific Tcell clones from different donors. Piesche et al. investigated theprocessing and presentation of SVN peptide epitopes from natural antigenby co-culturing of peptide-specific T cell clones with SVNprotein-pulsed DCs. Only the SVN peptide S₁₀ was able to cause specificT cell proliferation during exposure with recombinant SVN protein. Thiswas shown in three S₁₀-specific T cell clones from different donors. Nospecific proliferation in response to the natural antigen was detectedfor the PR₃-specific T cell clones.

Further, tumor antigens from apoptotic or necrotic tumor cells wereinternalized by APCs in vivo, processed independently of MHC II, andpresented to CD4+ T cells. For T cell recognition of the genuine S₁₀epitope, DCs with tumor cell lysates from various SVN-positive tumorcell lines were pulsed. For the S₁₀ epitope, direct in vitro recognitionof lysate-pulsed DCs from the tumor cell lines Karpas-422, Jurkat, andHL-60 was detected. This was shown in at least three S₁₀-specific T cellclones from different donors.

To show that the epitope S₁₀ can induce an immune response in cancerpatients the presence of the corresponding CD4+ T lymphocytes in theblood of tumor patients had to be confirmed. PBMCs from various patientswere isolated and stimulated with the S₁₀ peptide. For this purpose PBMCsamples were drawn from patients before beginning of treatment and afterthe start of cytotoxicstatic therapy, Monocytes and B cells contained inthe PBMC fraction were used as antigen-/peptide-presenting cells. Afterone week of culturing, the cells were analyzed with respect to theirpeptide-specific proliferation using a [³H]-thymidine incorporationassay. Of 13 tested patients, only three had a detectable proliferativeresponse in vitro.

The potential use of peptide epitopes in immunotherapy essentiallydepends on whether the peptide-specific CD4+ T lymphocytes respond tothe corresponding antigen. Recognition of the naturally processedprotein antigen in the form of “genuine” or “true” epitopes isinfluenced by various factors in principle.

Piesche showed that protein recognition was only detectable for the SVNepitope S10. For the other identified peptides (SVN: S₄₀, S₈₈; PR₃: P₅₈,P₂₁₆, P₂₃₅, and P₂₃₉) no protein recognition was detectable. Piesche etal. stated that it is important, during endosomal proteolysis, for thepresent sequence motifs not to be degraded, as in the case of “cryptic”epitopes. In contrast to MHC class I-restricted epitopes, MHC class IImolecules can take up peptides of variable length (12-28); therefore,proteolytic cleavage of the peptide epitopes into defined lengths is notrequired.

Surprisingly and in contrast to Piesche's epitopes, the inventors showin the present invention that another epitope, SEQ ID NO: 1, derivedfrom survivin which is shorter than S₈₈, but also overlapping, eliciteda strong immuno-response in 16 out of 19 patients in vivo. (See Example4). Due to the high polymorphism of the HLA-DR locus, this is also aproof of the highly promiscuous binding of peptide SEQ ID NO: 1 aspredicted, as an immune response can only be evoked by a peptide boundto an HLA molecule.

The importance of the cancer entities for which an overexpression ofsurvivin was described in the literature is illustrated by Table 1.Cancer indications for which overexpression of survivin are a commonlydescribed feature were accountable for over 415,000 deaths in 2007 (seeTable 1).

Piesche et al. (2006) showed in vitro the presence of appropriateprecursors for peptide S88 in three out of four donors with overlappingHLA-DR alleles. Here the body of evidence is too small to deduce apromiscuous binding of S₈₈ to HLA-DR, as the obtained results may beexplained by binding to two different HLA-DR alleles (e.g. DR3 and DR11,or DR1 and DR3, or DR11 and DR4). In addition, the stimulation indicesobtained by a quite unspecific proliferation assay ([³H]-thymidineincorporation) from whole PBMC cultures are quite low and a positivecontrol is missing (e.g. a mix of well-characterized, stronglyimmunogenic viral peptides) and appropriate negative controls(stimulation during proliferation assay with an irrelevant controlpeptide) are missing. The data on precursor frequencies were notconfirmed by a second type of assay.

WO 2007/036638 (“Wang et al”), amongst others, discloses survivinpeptides of the amino acid sequences:

 96-110 (LTLGEFLKLDRERAK; SEQ ID NO: 25);  99-113 (GEFLKLDRERAKNKI;SEQ ID NO: 26); and 102-116 (LKLDRERAKNKIAKE; SEQ ID NO: 27).

As a region binding HLA-molecules of MHC class II with “good” affinity(IC₅₀<1000 nM), the region 84 to 113 is described. Nevertheless, thepeptides as examined in Wang et al. show a very broad spectrum ofbinding towards the different HLA-molecules, and the binding evendiffers drastically within the region as described, when the peptidesare shifted in their sequence by one or two amino acids.

The peptide of the present invention of SEQ ID NO: 3 (TLGEFLKLDRERAKD;“BIR-002a” peptide) comprises a sequence of the BIR-002 peptide of thepresent invention of SEQ ID NO: 1, except that C-terminally, the peptideends with the amino acid aspartic acid (D) instead of asparagine (N).The peptide overlaps with the peptide S₈₈ of Piesche, which contains thelast three amino acids NKI. As mentioned above, the S₈₈ peptide wasinactive in a specific T cell proliferation assay during exposure withrecombinant SVN protein. In contrast, the BIR-002a peptide showed astrong MHC II-related immuno-response. Without wanting to be bound bytheory, it is assumed that an enzymatic conversion of the asparagineinto aspartic acid through an asparaginase takes place in vivo, and thusthe C-terminal amino acid is modified (and the peptide becomes activatedand/or further activated). Since the C-terminal asparagine of thePiesche-peptide S₈₈ is blocked by two amino acids, the peptide isinactive (further showing the importance of a single amino acid changein the activity of this peptide).

Furthermore, it was noted that the immuno-responses and activities ofother peptides comprising a C-terminal asparagine (such as, for example,SEQ ID NO: 1) may also depend on a C-terminal conversion into an acidamino acid, in particular aspartic acid. Thus, in one aspect of thepresent invention, the peptide according to SEQ ID NO: 1 may be seen asa “prodrug” for SEQ ID NO: 3, which provides the active peptideaccording to SEQ ID NO: 3 after enzymatic conversion. It should beunderstood that the present invention also encompasses chemicalconversion of the amino acid, particularly asparagine, and thespontaneous deamidation by the loss of one molecule of water.

Furthermore, the examples showing an activity for the peptide accordingto SEQ ID NO: 1 also support an activity for the modified peptideaccording to SEQ ID NO: 3.

It could furthermore be found in the context of the present inventionthat the solubilities of peptides in the area of the BIR-002 peptide(region 84 to 113) differ drastically for very similar peptides. It hasto be noted that in Wang et al., peptides in the region close to theBIR-002 peptide were actually insoluble, and binding studies could notbe performed.

The solubilities were determined as follows:

BIR-002 (SEQ ID No: 1): <32.9 mg/mL (acetate)

BIR-002a (SEQ ID No: 3) (D instead of N at the C-terminal end): <23.5mg/mL

BIR-014 (comparative peptide of Wang, SEQ ID NO: 25): <99.5 mg/mL

Yet another aspect of the present invention relates to an antibody thatspecifically binds to a human major histocompatibility complex (MHC)class I or II complexed with a HLA-restricted antigen (in the followingalso designate as “complex-specific antibody”). Yet another aspect ofthe present invention relates to a method of producing the antibodyspecifically binding to a human major histocompatibility complex (MHC)class I or II complexed with a HLA-restricted antigen, the methodcomprising: immunizing a genetically engineered non-human mammalcomprising cells expressing a human major histocompatibility complex(MHC) class I or II with a soluble form of a MHC class I or II moleculebeing complexed with the HLA-restricted antigen; isolating mRNAmolecules from antibody producing cells of the non-human mammal;producing a phage display library displaying protein molecules encodedby the mRNA molecules; and isolating at least one phage from said phagedisplay library, the at least one phage displaying the antibodyspecifically bindable to the human major histocompatibility complex(MHC) class I or II complexed with the HLA-restricted antigen.Respective methods for producing such antibodies and single chain classI major histocompatibility complexes, as well as other tools for theproduction of these antibodies are disclosed in WO 03/068201, WO2004/084798, WO 01/72768, WO 03/070752, and Cohen C J, Denkberg G, LevA, Epel M, Reiter Y. Recombinant antibodies with MHC-restricted,peptide-specific, T-cell receptor-like specificity: new tools to studyantigen presentation and TCR-peptide-MHC interactions. J Mol. Recognit.2003 September-Octber; 16(5):324-32; Denkberg G, Lev A, Eisenbach L,Benhar I, Reiter Y. Selective targeting of melanoma and APCs using arecombinant antibody with TCR-like specificity directed toward amelanoma differentiation antigen. J. Immunol. 2003 Sep. 1;171(5):2197-207; and Cohen C J, Sarig O, Yamano Y, Tomaru U, Jacobson S,Reiter Y. Direct phenotypic analysis of human MHC class I antigenpresentation: visualization, quantitation, and in situ detection ofhuman viral epitopes using peptide-specific, MHC-restricted humanrecombinant antibodies. J. Immunol. 2003 Apr. 15; 170(8):4349-61, whichfor the purposes of the present invention are all explicitlyincorporated by reference in their entireties.

Preferably, the antibody binds with a binding affinity of below 20nanomolar, preferably of below 10 nanomolar, to the complex, which isregarded as “specific” in the context of the present invention.

The term “antibody” is used herein in a broad sense and includes bothpolyclonal and monoclonal antibodies. In addition to intactimmunoglobulin molecules, also included in the term “antibodies” arefragments such as, but not limited to, Fabs and scFvs or polymers ofthose immunoglobulin molecules and humanized versions of immunoglobulinmolecules, so long as they exhibit any of the desired properties (e.g.,being a complex-specific antibody as above, delivery of a toxin to acancer cell expressing an cancer marker gene at an increased level,and/or inhibiting the activity of an cancer marker polypeptide, such assurvivin) described herein.

Whenever possible, the antibodies of the invention may be purchased fromcommercial sources. The antibodies of the invention may also begenerated using well-known methods. The skilled artisan will understandthat either full length cancer marker polypeptides or fragments thereofmay be used to generate the antibodies of the invention. A polypeptideto be used for generating an antibody of the invention may be partiallyor fully purified from a natural source, or may be produced usingrecombinant DNA techniques. For example, a cDNA encoding a survivinpolypeptide, or a fragment thereof, can be expressed in prokaryoticcells (e.g., bacteria) or eukaryotic cells (e.g., yeast, insect, ormammalian cells), after which the recombinant protein can be purifiedand used to generate a monoclonal or polyclonal antibody preparationthat specifically bind the cancer marker polypeptide used to generatethe antibody. Complex-specific antibodies will usually be generated asabove.

One of skill in the art will know that the generation of two or moredifferent sets of monoclonal or polyclonal antibodies maximizes thelikelihood of obtaining an antibody with the specificity and affinityrequired for its intended use (e.g., ELISA, immunohistochemistry, invivo imaging, immunotoxin therapy). The antibodies are tested for theirdesired activity by known methods, in accordance with the purpose forwhich the antibodies are to be used (e.g., ELISA, immunohistochemistry,immunotherapy, etc.; for further guidance on the generation and testingof antibodies, see, e.g., Harlow and Lane, Antibodies: A LaboratoryManual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,1988). For example, the antibodies may be tested in ELISA assays,Western blots, immunohistochemical staining of formalin-fixed cancersamples or frozen tissue sections. After their initial in vitrocharacterization, antibodies intended for therapeutic or in vivodiagnostic use are tested according to known clinical testing methods.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a substantially homogeneous population of antibodies,i.e.; the individual antibodies comprising the population are identicalexcept for possible naturally occurring mutations that may be present inminor amounts. The monoclonal antibodies herein specifically include“chimeric” antibodies in which a portion of the heavy and/or light chainis identical with or homologous to corresponding sequences in antibodiesderived from a particular species or belonging to a particular antibodyclass or subclass, while the remainder of the chain(s) is identical withor homologous to corresponding sequences in antibodies derived fromanother species or belonging to another antibody class or subclass, aswell as fragments of such antibodies, so long as they exhibit thedesired antagonistic activity (U.S. Pat. No. 4,816,567).

Monoclonal antibodies of the invention may be prepared using hybridomamethods. In a hybridoma method, a mouse or other appropriate hostanimal, is typically immunized with an immunizing agent to elicitlymphocytes that produce or are capable of producing antibodies thatwill specifically bind to the immunizing agent. Alternatively, thelymphocytes may be immunized in vitro.

The monoclonal antibodies may also be made by recombinant DNA methods,such as those described in U.S. Pat. No. 4,816,567. DNA encoding themonoclonal antibodies of the invention can be readily isolated andsequenced using conventional procedures (e.g., by using oligonucleotideprobes that are capable of binding specifically to genes encoding theheavy and light chains of murine antibodies).

In vitro methods are also suitable for preparing monovalent antibodies.Digestion of antibodies to produce fragments thereof, particularly, Fabfragments, can be accomplished using routine techniques known in theart. For instance, digestion can be performed using papain. Examples ofpapain digestion are described in WO 94/29348 published Dec. 22, 1994and U.S. Pat. No. 4,342,566. Papain digestion of antibodies typicallyproduces two identical antigen binding fragments, called Fab fragments,each with a single antigen binding site, and a residual Fe fragment.Pepsin treatment yields a fragment that has two antigen combining sitesand is still capable of cross-linking antigen.

The antibody fragments, whether attached to other sequences or not, canalso include insertions, deletions, substitutions, or other selectedmodifications of particular regions or specific amino acids residues,provided the activity of the fragment is not significantly altered orimpaired compared to the non-modified antibody or antibody fragment.These modifications can provide for some additional property, such as toremove/add amino acids capable of disulfide bonding, to increase itsbio-longevity, to alter its secretory characteristics, etc. In any case,the antibody fragment must possess a bioactive property, such as bindingactivity, regulation of binding at the binding domain, etc. Functionalor active regions of the antibody may be identified by mutagenesis of aspecific region of the protein, followed by expression and testing ofthe expressed polypeptide. Such methods are readily apparent to askilled practitioner in the art and can include site-specificmutagenesis of the nucleic acid encoding the antibody fragment.

The antibodies of the invention may further comprise humanizedantibodies or human antibodies. Humanized forms of non-human (e.g.,murine) antibodies are chimeric immunoglobulins, immunoglobulin chainsor fragments thereof (such as Fv, Fab, Fab′ or other antigen-bindingsubsequences of antibodies) which contain minimal sequence derived fromnon-human immunoglobulin. Humanized antibodies include humanimmunoglobulins (recipient antibody) in which residues from acomplementary determining region (CDR) of the recipient are replaced byresidues from a CDR of a non-human species (donor antibody) such asmouse, rat or rabbit having the desired specificity, affinity andcapacity. In some instances, Fv framework (FR) residues of the humanimmunoglobulin are replaced by corresponding non-human residues.Humanized antibodies may also comprise residues that are found neitherin the recipient antibody nor in the imported CDR or frameworksequences. In general, the humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the CDR regions correspond to thoseof a non-human immunoglobulin and all or substantially all of the FRregions are those of a human immunoglobulin consensus sequence. Thehumanized antibody optimally also will comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin.

Methods for humanizing non-human antibodies are well known in the art.Generally, a humanized antibody has one or more amino acid residuesintroduced into it from a source which is non-human. These non-humanamino acid residues are often referred to as “import” residues, whichare typically taken from an “import” variable domain. Humanization canbe essentially performed by substituting rodent CDRs or CDR sequencesfor the corresponding sequences of a human antibody. Accordingly, such“humanized” antibodies are chimeric antibodies (U.S. Pat. No.4,816,567), wherein substantially less than an intact human variabledomain has been substituted by the corresponding sequence from anon-human species. In practice, humanized antibodies are typically humanantibodies in which some CDR residues and possibly some FR residues aresubstituted by residues from analogous sites in rodent antibodies.

Transgenic animals (e.g., mice) that are capable, upon immunization, ofproducing a full repertoire of human antibodies in the absence ofendogenous immunoglobulin production can be employed. For example, ithas been described that the homozygous deletion of the antibody heavychain joining region gene in chimeric and germ-line mutant mice resultsin complete inhibition of endogenous antibody production. Transfer ofthe human germ-line immunoglobulin gene array in such germ-line mutantmice will result in the production of human antibodies upon antigenchallenge. Human antibodies can also be produced in phage displaylibraries as, for example, described above for the complex-specificantibodies.

Antibodies of the invention are preferably administered to a subject ina pharmaceutically acceptable carrier. Typically, an appropriate amountof a pharmaceutically-acceptable salt is used in the formulation torender the formulation isotonic. Examples of thepharmaceutically-acceptable carrier include saline, Ringer's solutionand dextrose solution. The pH of the solution is preferably from about 5to about 8, and more preferably from about 7 to about 7.5. Additionalcarriers include sustained release preparations such as semipermeablematrices of solid hydrophobic polymers containing the antibody, whichmatrices are in the form of shaped articles, e.g., films, liposomes ormicroparticles. It will be apparent to those persons skilled in the artthat certain carriers may be more preferable depending upon, forinstance, the route of administration and concentration of antibodybeing administered.

The antibodies can be administered to the subject, patient, or cell byinjection (e.g., intravenous, intraperitoneal, subcutaneous,intramuscular), or by other methods such as infusion that ensure itsdelivery to the bloodstream in an effective form. The antibodies mayalso be administered by intratumoral or peritumoral routes, to exertlocal as well as systemic therapeutic effects. Local or intravenousinjection is preferred.

Effective dosages and schedules for administering the antibodies may bedetermined empirically, and making such determinations is within theskill in the art. Those skilled in the art will understand that thedosage of antibodies that must be administered will vary depending on,for example, the subject that will receive the antibody, the route ofadministration, the particular type of antibody used and other drugsbeing administered. Antibodies in Human Diagnosis and Therapy, Haber etal, eds. Raven Press, New York (1977) pp. 365-389. A typical dailydosage of the antibody used alone might range from about 1 (μg/kg to upto 100 mg/kg of body weight or more per day) depending on the factorsmentioned above. Following administration of an antibody for treatingcancer, the efficacy of the therapeutic antibody can be assessed invarious ways well known to the skilled practitioner. For instance, thesize, number, and/or distribution of cancer in a subject receivingtreatment may be monitored using standard tumor imaging techniques. Atherapeutically-administered antibody that arrests tumor growth, resultsin tumor shrinkage, and/or prevents the development of new tumors,compared to the disease course that would occurs in the absence ofantibody administration, is an efficacious antibody for treatment ofcancers.

The antibodies may also be used for in vivo diagnostic assays.Generally, the antibody is labeled with a radionucleotide (such as¹¹¹In, ₉₉Tc, ¹⁴C, ¹³¹I, ³H, ³²P or ³⁵S) so that the tumor can belocalized using immunoscintiography. In one embodiment, antibodies orfragments thereof bind to the extracellular domains of two or morecancer targets and the affinity value (Kd) is less than 1×10 μM.

Antibodies for diagnostic use may be labeled with probes suitable fordetection by various imaging methods. Methods for detection of probesinclude, but are not limited to, fluorescence, light, confocal andelectron microscopy; magnetic resonance imaging and spectroscopy;fluoroscopy, computed tomography and positron emission tomography.Suitable probes include, but are not limited to, fluorescein, rhodamine,eosin and other fluorophores, radioisotopes, gold, gadolinium and otherlanthanides, paramagnetic iron, fluorine-18 and other positron-emittingradionuclides. Additionally, probes may be bi- or multi-functional andbe detectable by more than one of the methods listed. These antibodiesmay be directly or indirectly labeled with the probes. Attachment ofprobes to the antibodies includes covalent attachment of the probe,incorporation of the probe into the antibody, and the covalentattachment of a chelating compound for binding of probe, amongst otherswell recognized in the art. For immunohistochemistry, the disease tissuesample may be fresh or frozen or may be embedded in paraffin and fixedwith a preservative such as formalin. The fixed or embedded sectioncontains the sample are contacted with a labeled primary antibody andsecondary antibody, wherein the antibody is used to detect the desiredprotein expressed in situ.

The present invention thus provides a peptide comprising a sequence thatis selected from the group of SEQ ID NO: 1 to SEQ ID NO: 3 or a variantthereof which is 85% homologous to SEQ ID NO: 1 to SEQ ID NO: 3 or avariant thereof that will induce T cells cross-reacting with thepeptide. In a preferred embodiment, the variant is 95% homologous or 95%identical to SEQ ID NO: 1 or SEQ ID NO: 3, as long as the variant willinduce T cells cross-reacting with the peptide.

In a preferred embodiment for the treatment of renal cell carcinoma thepeptide of the SEQ ID NO: 1 and/or SEQ ID NO: 2 and/or SEQ ID NO: 3 isused in combination with at least two of the peptides with SEQ ID NO: 4to SEQ ID NO: 13 and SEQ ID NO: 24. The peptide of the SEQ ID NO: 1 toSEQ ID NO: 3 may thereby be administered separately or together with theother peptides in one formulation.

SEQ Internal ID Sequence ID Antigen Sequence NO: IMA-MMP-001 MatrixSQDDIKGIQKLYGKRS  4 metallopro-  teinase 7 IMA-ADF-002 AdipophilinVMAGDIYSV  5 IMA-ADF-001 Adipophilin SVASTITGV  6 IMA-APO-001Apolipoprotein ALADGVQKV  7 L1 IMA-CCN-001 Cyclin D1 LLGATCMFV  8IMA-GUC-001 GUCY1A3 SVFAGVVGV  9 IMA-K67-001 KIAA0367 ALFDGDPHL 10IMA-MET-001 c-met YVDPVITSI 11 proto-oncogene IMA-MUC-001 MUC1 STAPPVHNV12 IMA-RGS-001 RGS-5 LAALPHSCL 13 IMA-HBV-001 HBV FLPSDFFPSV 14IMA-NCAN-001 Neurocan VLCGPPPAV 24

A detailed description of the peptides and the antigens provided aboveis disclosed in WO 2007/028573.

In a preferred embodiment for the treatment of colon cancer, the peptideof the SEQ ID NO: 1 to SEQ ID NO: 3 is used in combination with at leasttwo of the peptides with SEQ ID NO: 15 to 24, 4, 8, 11 or 12. Thepeptide of the SEQ ID NO: 1 to SEQ ID NO: 3 may thereby be administeredseparately or together with the other peptides in one formulation.

SEQ ID Peptide Gene binds to NO: ID Sequence Symbol Function MHC 15C20-001 ALSNLEVTL C20orf42 implicated in HLA-A*02 linking actincytoskeleton to ECM 16 NOX-001 ILAPVILYI NOX1 NADPH oxidase HLA-A*02 17ODC-001 ILDQKINEV ODC1 Ornithine HLA-A*02 decarboxylase 18 PCN-001KLMDLDVEQL PCNA DNA polymerase HLA-A*02 delta auxiliary protein 19TGFBI-001 ALFVRLLALA TGFBI transforming HLA-A*02 growth factor,beta-induced 20 TOP-001 KIFDEILVNA TOP2A/ Topoisomerase HLA-A*02 TOP2B21 TGFBI-004 TPPIDAHTRNLLRNH TGFBI transforming HLA-DR growth factor,beta-induced 22 CEA-006 SPQYSWRINGIPQQHT CEACAM5 Carcinoembryonic HLA-DRantigen  8 CCN-001 LLGATCMFV CCND1 Cyclin D1 HLA-A*02 12 MUC-001STAPPVHNV MUC1 Mucin 1 HLA-A*02  4 MMP-001 SQDDIKGIQKLYGKRS MMP7Metalloproteinase 7 HLA-DR 23 CEA-004 YLSGANLNL CEACAM5variant of CEA peptide HLA-A*02 11 MET-001 YVDPVITSI METmet proto-oncogene HLA-A*02

A detailed description of the peptides and the antigens provided aboveis disclosed in EP07014796.2 and U.S. 60/953,161.

The peptides of the invention have the ability to bind to a molecule ofthe human major histocompatibility complex (MHC) class-I or -II.

In the present invention, the term “homologous” refers to the degree ofidentity between sequences of two amino acid sequences, i.e. peptide orpolypeptide sequences. The aforementioned “homology” is determined bycomparing two sequences aligned under optimal conditions over thesequences to be compared. The sequences to be compared herein may havean addition or deletion (for example, gap and the like) in the optimumalignment of the two sequences. Such a sequence homology can becalculated by creating an alignment using, for example, the ClustalWalgorithm (Nucleic Acid Res., 22(22): 4673 4680 (1994). Commonlyavailable sequence analysis software, more specifically, Vector NTI,GENETYX or analysis tools provided by public databases.

A person skilled in the art will be able to assess, whether T cellsinduced by a variant of a specific peptide will be able to cross-reactwith the peptide itself (Fong et al., 2001); (Zaremba et al., 1997;Colombetti et al., 2006; Appay et al., 2006).

By a “variant” of the given amino acid sequence the inventors mean thatthe side chains of, for example, one or two of the amino acid residuesare altered (for example by replacing them with the side chain ofanother naturally occurring amino acid residue or some other side chain)such that the peptide is still able to bind to an HLA molecule insubstantially the same way as a peptide consisting of the given aminoacid sequence in SEQ ID NO:1 to 24. For example, a peptide may bemodified so that it at least maintains, if not improves, the ability tointeract with and bind to the binding groove of a suitable MHC molecule,such as HLA-A*02 or -DR, and in that way it at least maintains, if notimproves, the ability to bind to the TCR of activated CTL. These CTL cansubsequently cross-react with cells and kill cells that express apolypeptide that contains the natural amino acid sequence of the cognatepeptide as defined in the aspects of the invention. As can be derivedfrom the scientific literature (Rammensee et al., 1997) and databases(Rammensee et al., 1999), certain positions of HLA binding peptides aretypically anchor residues forming a core sequence fitting to the bindingmotif of the HLA receptor, which is defined by polar, electrophysical,hydrophobic and spatial properties of the polypeptide chainsconstituting the binding groove. Thus one skilled in the art would beable to modify the amino acid sequences set forth in SEQ ID NO:1 to 24,by maintaining the known anchor residues, and would be able to determinewhether such variants maintain the ability to bind MHC class I or IImolecules. The variants of the present invention retain the ability tobind to the TCR of activated CTL, which can subsequently cross-reactwith- and kill cells that express a polypeptide containing the naturalamino acid sequence of the cognate peptide as defined in the aspects ofthe invention.

Those amino acid residues that do not substantially contribute tointeractions with the T-cell receptor can be modified by replacementwith another amino acid whose incorporation does not substantiallyaffect T-cell reactivity and does not eliminate binding to the relevantMHC. Thus, apart from the proviso given, the peptide of the inventionmay be any peptide (by which term the inventors include oligopeptide orpolypeptide), which includes the amino acid sequences or a portion orvariant thereof as given.

TABLE 5 Variants and motif of the peptide according to SEQ ID NO: 24 SEQID Position NO NCAN 1 2 3 4 5 6 7 8 9 24 Peptide V L C G P P P A V code73 Variants M L 74 I L 75 E K 76 I A G I I A E 77 L Y P K L Y 78 F F T YT H 79 K P N 80 M M F 81 Y S V 82 V R 83 M L

It is furthermore known for MHC-class II-presented peptides that thesepeptides are composed of a “core sequence” having an amino acid sequencefitting to a certain HLA-allele-specific motif and, optionally, N-and/or C-terminal extensions that do not interfere with the function ofthe core sequence (i.e. are deemed as irrelevant for the interaction ofthe peptide and all or a subset of T cell clones recognizing the naturalcounterpart). The N- and/or C-terminal extensions can, for example, bebetween 1 to 10 amino acids in length, respectively. These peptides canbe used either directly to load MHC class II molecules or the sequencecan be cloned into the vectors according to the description hereinbelow. As these peptides constitute the final product of the processingof larger peptides within the cell, longer peptides can be used as well.The peptides of the invention may be of any size, but typically they maybe less than 100,000 in molecular weight, preferably less than 50,000,more preferably less than 10,000 and typically about 5,000. In terms ofthe number of amino acid residues, the peptides of the invention mayhave fewer than 1,000 residues, preferably fewer than 500 residues, morepreferably fewer than 100, more preferably fewer than 100 and mostpreferably between 30 and 8 residues. Accordingly, the present inventionalso provides peptides and variants thereof wherein said peptide orvariant has an overall length of between 8 and 100, preferably between 8and 30, and most preferred between 8 and 16, namely 8, 9, 10, 11, 12,13, 14, 15, 16 amino acids.

For MHC class II restricted peptides, several different peptides withthe same core sequence may be presented in the MHC molecule. As theinteraction with the recognizing T (helper) cell is defined by a coresequence of 9 to 11 amino acids, several length variants may berecognized by the same T (helper) cell clone. Thus, several differentlengths variants of a core binding sequence may be used for directloading of MHC class II molecules without the need for furtherprocessing and trimming at the N- or C-terminal ends. Correspondingly,naturally occurring or artificial variants that induce T cellscross-reacting with a peptide of the invention are often lengthvariants.

If a peptide that is longer than around 12 amino acid residues is useddirectly to bind to a MHC class II molecule, it is preferred that theresidues that flank the core HLA binding region are residues that do notsubstantially affect the ability of the peptide to bind specifically tothe binding groove of the MHC class II molecule or to present thepeptide to the T (-helper) cell. However, as already indicated above, itwill be appreciated that larger peptides may be used, e.g. when encodedby a polynucleotide, since these larger peptides may be fragmented bysuitable antigen-presenting cells. However, in same cases it has beenshown that the core sequence flanking regions can influence the peptidebinding to MHC class II molecule or the interaction of the dimericMHC:peptide complex with the TCR in both directions compared to areference peptide with the same core sequence. Intramolecular tertiarystructures within the peptide (e.g. loop formation) normally decreasethe affinities to the MHC or TCR. Intermolecular interactions of theflanking regions with parts of the MHC or TCR beside the peptide bindinggrooves may stabilize the interaction. These changes in affinity canhave a dramatic influence on the potential of a MHC class II peptide toinduce T (helper) cell responses.

It is also possible, that MHC class I epitopes, although usually between8-10 amino acids long, are generated by peptide processing from longerpeptides or proteins that include the actual epitope. It is preferredthat the residues that flank the actual epitope are residues that do notsubstantially affect proteolytic cleavage necessary to expose the actualepitope during processing.

Accordingly, the present invention also provides peptides and variantsof MHC class I epitopes wherein the peptide or variant has an overalllength of between 8 and 100, preferably between 8 and 30, and mostpreferred between 8 and 16, namely 8, 9, 10, 11, 12, 13, 14, 15, 16amino acids.

Of course, the peptide or variant according to the present inventionwill have the ability to bind to a molecule of the human majorhistocompatibility complex (MHC) class I or II. Binding of a peptide ora variant to a MHC complex may be tested by methods known in the art,for example those described in the literature for different MHC class IIalleles (e.g. Vogt et al., 1994; Malcherek et al., 1994; Manici et al.,1999; Hammer et al., 1995; Tompkins et al., 1993; Boyton et al., 1998).

In a particularly preferred embodiment of the invention the peptideconsists or consists essentially of an amino acid sequence according toSEQ ID NO: 1 to SEQ ID NO: 3.

The peptides according to the present invention can also consist of acontinuous stretch of amino acids as depicted in SEQ ID NO: 1 to 3,wherein said stretch is a part of said sequence having a length of atleast 8 amino acids (e.g. 8, 9, 10, 11, 12, 13, 14, 15, or 16), as longas a core sequence is present in said peptide, rendering it functionalin eliciting an immuno-response as described herein.

“Consisting essentially of” shall mean that a peptide according to thepresent invention, in addition to the sequence according to any of SEQID NO: 1 to SEQ ID NO: 3 or a variant thereof contains additional N-and/or C-terminally located stretches of amino acids that are notnecessarily forming part of the peptide that functions as an epitope forMHC molecules epitope.

Nevertheless, these stretches can be important to provide an efficientintroduction of the peptide according to the present invention into thecells. In one embodiment of the present invention, the peptide is afusion protein that comprises, for example, the 80 N-terminal aminoacids of the HLA-DR antigen-associated invariant chain (p33, in thefollowing “Ii”) as derived from the NCBI, GenBank Accession-numberX00497 (Strubin, M. et al 1984).

Examples of further preferred peptides include peptides having aspecific HLA-subtype and that are capable of stimulating CD8 cells, andwherein the peptide comprises the specific anchor amino acid-motif asdepicted in the following Table 6.

TABLE 6 HLA-subtypes and anchor motifs of preferred peptide according toSEQ ID NO: 24 HLA- Position Peptide subtype 1 2 3 4 5 6 7 8 9 24 A*02Peptide V L C G P P P A V Code Anchor x L x x x x x x V motif

In addition, the peptide or variant may be modified further to improvestability and/or binding to MHC molecules in order to elicit a strongerimmune response. Methods for such an optimization of a peptide sequenceare well known in the art and include, for example, the introduction ofreverse peptide bonds or non-peptide bonds.

In a reverse peptide bond amino acid residues are not joined by peptide(—CO—NH—) linkages but the peptide bond is reversed. Such retro-inversopeptidomimetics may be made using methods known in the art, for examplesuch as those described in Meziere et al (1997) J. Immunol. 159,3230-3237, incorporated herein by reference. This approach involvesmaking pseudopeptides containing changes involving the backbone, and notthe orientation of side chains. Meziere et al (1997) show that for MHCbinding and T helper cell responses, these pseudopeptides are useful.Retro-inverse peptides, which contain NH—CO bonds instead of CO—NHpeptide bonds, are much more resistant to proteolysis.

A non-peptide bond is, for example, —CH₂—NH, —CH₂S—, —CH₂CH₂—, —CH═CH—,—COCH₂—, —CH(OH)CH₂—, and —CH₂SO—. U.S. Pat. No. 4,897,445 provides amethod for the solid phase synthesis of non-peptide bonds (—CH₂—NH) inpolypeptide chains which involves polypeptides synthesized by standardprocedures and the non-peptide bond synthesized by reacting an aminoaldehyde and an amino acid in the presence of NaCNBH₃.

Peptides comprising the sequences described above may be synthesizedwith additional chemical groups present at their amino and/or carboxytermini, to enhance the stability, bioavailability, and/or affinity ofthe peptides. For example, hydrophobic groups such as carbobenzoxyl,dansyl, or t-butyloxycarbonyl groups may be added to the peptides' aminotermini. Likewise, an acetyl group or a 9-fluorenylmethoxy-carbonylgroup may be placed at the peptides' amino termini. Additionally, thehydrophobic group, t-butyloxycarbonyl, or an amido group may be added tothe peptides' carboxy termini.

Further, the peptides of the invention may be synthesized to alter theirsteric configuration. For example, the D-isomer of one or more of theamino acid residues of the peptide may be used, rather than the usualL-isomer. Still further, at least one of the amino acid residues of thepeptides of the invention may be substituted by one of the well knownnon-naturally occurring amino acid residues. Alterations such as thesemay serve to increase the stability, bioavailability and/or bindingaction of the peptides of the invention.

Similarly, a peptide or variant of the invention may be modifiedchemically by reacting specific amino acids either before or aftersynthesis of the peptide. Examples for such modifications are well knownin the art and are summarized e.g. in R. Lundblad, Chemical Reagents forProtein Modification, 3^(rd) ed. CRC Press, 2005, which is incorporatedherein by reference. Chemical modification of amino acids includes butis not limited to, modification by acylation, amidination,pyridoxylation of lysine, reductive alkylation, trinitrobenzylation ofamino groups with 2,4,6-trinitrobenzene sulphonic acid (TNBS), amidemodification of carboxyl groups and sulphydryl modification by performicacid oxidation of cysteine to cysteic acid, formation of mercurialderivatives, formation of mixed disulphides with other thiol compounds,reaction with maleimide, carboxymethylation with iodoacetic acid oriodoacetamide and carbamoylation with cyanate at alkaline pH, althoughwithout limitation thereto. In this regard, the skilled person isreferred to Chapter 15 of Current Protocols In Protein Science, Eds.Coligan et al. (John Wiley & Sons NY 1995-2000) for more extensivemethodology relating to chemical modification of proteins.

Briefly, modification of e.g. arginyl residues in proteins is oftenbased on the reaction of vicinal dicarbonyl compounds such asphenylglyoxal, 2,3-butanedione, and 1,2-cyclohexanedione to form anadduct. Another example is the reaction of methylglyoxal with arginineresidues. Cysteine can be modified without concomitant modification ofother nucleophilic sites such as lysine and histidine. As a result, alarge number of reagents are available for the modification of cysteine.The websites of companies such as Sigma-Aldrich provide information onspecific reagents.

Selective reduction of disulfide bonds in proteins is also common.Disulfide bonds can be formed and oxidized during the heat treatment ofbiopharmaceuticals.

Woodward's Reagent K may be used to modify specific glutamic acidresidues. N-(3-(dimethylamino)propyl)-N′-ethylcarbodiimide can be usedto form intra-molecular crosslinks between a lysine residue and aglutamic acid residue.

For example, diethylpyrocarbonate is a reagent for the modification ofhistidyl residues in proteins. Histidine can also be modified using4-hydroxy-2-nonenal.

The reaction of lysine residues and other α-amino groups is, forexample, useful in binding of peptides to surfaces or the cross-linkingof proteins/peptides. Lysine is the site of attachment ofpoly(ethylene)glycol and the major site of modification in the glycationof proteins. Methionine residues in proteins can be modified with e.g.iodoacetamide, bromoethylamine, and chloramine T. Tetranitromethane andN-acetylimidazole can be used for the modification of tyrosyl residues.Cross-linking via the formation of dityrosine can be accomplished withhydrogen peroxide/copper ions.

Recent studies on the modification of tryptophan have usedN-bromosuccinimide, 2-hydroxy-5-nitrobenzyl bromide or3-bromo-3-methyl-2-(2-nitrophenylmercapto)-3H-indole (BPNS-skatole).

Successful modification of therapeutic proteins and peptides with PEG isoften associated with an extension of circulatory half-life whilecross-linking of proteins with glutaraldehyde, polyethyleneglycoldiacrylate and formaldehyde is used for the preparation of hydrogels.Chemical modification of allergens for immunotherapy is often achievedby carbamylation with potassium cyanate.

A peptide or variant, wherein the peptide is modified or includesnon-peptide bonds is a preferred embodiment of the invention. Generally,peptides and variants (at least those containing peptide linkagesbetween amino acid residues) may be synthesized by the Fmoc-polyamidemode of solid-phase peptide synthesis as disclosed by Lu et al (1981)and references therein. Temporary N-amino group protection is affordedby the 9-fluorenylmethyloxycarbonyl (Fmoc) group. Repetitive cleavage ofthis highly base-labile protecting group is done using 20% piperidine inN,N-dimethylformamide. Side-chain functionalities may be protected astheir butyl ethers (in the case of serine threonine and tyrosine), butylesters (in the case of glutamic acid and aspartic acid),butyloxycarbonyl derivative (in the case of lysine and histidine),trityl derivative (in the case of cysteine) and4-methoxy-2,3,6-trimethylbenzenesulphonyl derivative (in the case ofarginine). Where glutamine or asparagine are C-terminal residues, use ismade of the 4,4′-dimethoxybenzhydryl group for protection of the sidechain amido functionalities. The solid-phase support is based on apolydimethyl-acrylamide polymer constituted from the three monomersdimethylacrylamide (backbone-monomer), bisacryloylethylene diamine(cross linker) and acryloylsarcosine methyl ester (functionalizingagent). The peptide-to-resin cleavable linked agent used is theacid-labile 4-hydroxymethyl-phenoxyacetic acid derivative. All aminoacid derivatives are added as their preformed symmetrical anhydridederivatives with the exception of asparagine and glutamine, which areadded using a reversedN,N-dicyclohexyl-carbodiimide/lhydroxybenzotriazole mediated couplingprocedure. All coupling and deprotection reactions are monitored usingninhydrin, trinitrobenzene sulphonic acid or isotin test procedures.Upon completion of synthesis, peptides are cleaved from the resinsupport with concomitant removal of side-chain protecting groups bytreatment with 95% trifluoroacetic acid containing a 50% scavenger mix.Scavengers commonly used include ethandithiol, phenol, anisole andwater, the exact choice depending on the constituent amino acids of thepeptide being synthesized. Also a combination of solid phase andsolution phase methodologies for the synthesis of peptides is possible(see, for example, Bruckdorfer et al. 2004, and the references as citedtherein).

Trifluoroacetic acid is removed by evaporation in vacuo, with subsequenttrituration with diethyl ether affording the crude peptide. Anyscavengers present are removed by a simple extraction procedure which onlyophilisation of the aqueous phase affords the crude peptide free ofscavengers. Reagents for peptide synthesis are generally available frome.g. Calbiochem-Novabiochem (UK) Ltd, Nottingham NG7 2QJ, UK.

Purification may be performed by any one, or a combination of,techniques such as re-crystallization, size exclusion chromatography,ion-exchange chromatography, hydrophobic interaction chromatography and(usually) reverse-phase high performance liquid chromatography usinge.g. acetonitril/water gradient separation.

Analysis of peptides may be carried out using thin layer chromatography,electrophoresis, in particular capillary electrophoresis, solid phaseextraction (CSPE), reverse-phase high performance liquid chromatography,amino-acid analysis after acid hydrolysis and by fast atom bombardment(FAB) mass spectrometric analysis, as well as MALDI and ESI-Q-TOF massspectrometric analysis.

A further aspect of the invention provides a nucleic acid (for example apolynucleotide) encoding a peptide or peptide variant of the invention.The polynucleotide may be, for example, DNA, cDNA, PNA, CNA, RNA orcombinations thereof, either single- and/or double-stranded, or nativeor stabilized forms of polynucleotides, such as, for example,polynucleotides with a phosphorothioate backbone and it may or may notcontain introns so long as it codes for the peptide. Of course, onlypeptides that contain naturally occurring amino acid residues joined bynaturally occurring peptide bonds are encodable by a polynucleotide. Astill further aspect of the invention provides an expression vectorcapable of expressing a polypeptide or peptide according to theinvention.

A variety of methods have been developed to link polynucleotides,especially DNA, to vectors for example via complementary cohesivetermini. For instance, complementary homopolymer tracts can be added tothe DNA segment to be inserted to the vector DNA. The vector and DNAsegment are then joined by hydrogen bonding between the complementaryhomopolymeric tails to form recombinant DNA molecules.

Synthetic linkers containing one or more restriction sites provide analternative method of joining the DNA segment to vectors. Syntheticlinkers containing a variety of restriction endonuclease sites arecommercially available from a number of sources including InternationalBiotechnologies Inc, New Haven, Conn., USA.

A desirable method of modifying the DNA encoding the polypeptide orpeptide of the invention uses the polymerase chain reaction as disclosedby (Saiki et al (1988)). This method may be used for introducing the DNAinto a suitable vector, for example by engineering in suitablerestriction sites, or it may be used to modify the DNA in other usefulways as is known in the art. If viral vectors are used, pox- oradenovirus vectors are preferred.

The DNA (or in the case of retroviral vectors, RNA) may then beexpressed in a suitable host to produce a polypeptide comprising thepeptide or variant of the invention. Thus, the DNA encoding the peptideor variant of the invention may be used in accordance with knowntechniques, appropriately modified in view of the teachings containedherein, to construct an expression vector, which is then used totransform an appropriate host cell for the expression and production ofthe polypeptide of the invention. Such techniques include thosedisclosed in U.S. Pat. Nos. 4,440,859, 4,530,901, 4,582,800, 4,677,063,4,678,751, 4,704,362, 4,710,463, 4,757,006, 4,766,075, and 4,810,648.

The DNA (or in the case of retroviral vectors, RNA) encoding thepolypeptide or peptide constituting the compound of the invention may bejoined to a wide variety of other DNA sequences for introduction into anappropriate host. The companion DNA will depend upon the nature of thehost, the manner of the introduction of the DNA into the host, andwhether episomal maintenance or integration is desired.

Generally, the DNA is inserted into an expression vector, such as aplasmid, in proper orientation and correct reading frame for expression.If necessary, the DNA may be linked to the appropriate transcriptionaland translational regulatory control nucleotide sequences recognized bythe desired host, although such controls are generally available in theexpression vector. The vector is then introduced into the host throughstandard techniques. Generally, not all of the hosts will be transformedby the vector. Therefore, it will be necessary to select for transformedhost cells. One selection technique involves incorporating into theexpression vector a DNA sequence, with any necessary control elements,that codes for a selectable trait in the transformed cell, such asantibiotic resistance.

Alternatively, the gene for such selectable trait can be on anothervector, which is used to co-transform the desired host cell. Host cellsthat have been transformed by the recombinant DNA of the invention arethen cultured for a sufficient time and under appropriate conditionsknown to those skilled in the art in view of the teachings disclosedherein to permit the expression of the polypeptide, which can then berecovered.

Many expression systems are known, including bacteria (for example E.coli and Bacillus subtilis), yeasts (for example Saccharomycescerevisiae), filamentous fungi (for example Aspergillus spec.), plantcells, animal cells and insect cells. Preferably, the system can bemammalian cells such as CHO cells available from the ATCC Cell BiologyCollection.

A typical mammalian cell vector plasmid for constitutive expressioncomprises the CMV or SV40 promoter with a suitable poly A tail and aresistance marker, such as neomycin. One example is pSVL available fromPharmacia, Piscataway, NJ, USA. An example of an inducible mammalianexpression vector is pMSG, also available from Pharmacia. Useful yeastplasmid vectors are pRS403-406 and pRS413-416 and are generallyavailable from Stratagene Cloning Systems, La Jolla, CA 92037, USA.Plasmids pRS403, pRS404, pRS405 and pRS406 are Yeast Integratingplasmids (YIps) and incorporate the yeast selectable markers HIS3, TRP1,LEU2 and URA3. Plasmids pRS413-416 are Yeast Centromere plasmids (Ycps).CMV promoter-based vectors (for example from Sigma-Aldrich) providetransient or stable expression, cytoplasmic expression or secretion, andN-terminal or C-terminal tagging in various combinations of FLAG,3xFLAG, c-myc or MAT. These fusion proteins allow for detection,purification and analysis of recombinant protein. Dual-tagged fusionsprovide flexibility in detection.

The strong human cytomegalovirus (CMV) promoter regulatory region drivesconstitutive protein expression levels as high as 1 mg/L in COS cells.For less potent cell lines, protein levels are typically ˜0.1 mg/L. Thepresence of the SV40 replication origin will result in high levels ofDNA replication in SV40 replication permissive COS cells. CMV vectors,for example, can contain the pMB1 (derivative of pBR322) origin forreplication in bacterial cells, the b-lactamase gene for ampicillinresistance selection in bacteria, hGH polyA, and the f1 origin. Vectorscontaining the preprotrypsin leader (PPT) sequence can direct thesecretion of FLAG fusion proteins into the culture medium forpurification using ANTI-FLAG antibodies, resins, and plates. Othervectors and expression systems are well known in the art for use with avariety of host cells.

The present invention also relates to a host cell transformed with apolynucleotide vector construct of the present invention. The host cellcan be either prokaryotic or eukaryotic. Bacterial cells may bepreferred prokaryotic host cells in some circumstances and typically area strain of E. coli such as, for example, the E. coli strains DH5available from Bethesda Research Laboratories Inc., Bethesda, Md., USA,and RR1 available from the American Type Culture Collection (ATCC) of10801 University Boulevard, Manassas, Va. 20110-2209 (No ATCC 31343).Preferred eukaryotic host cells include yeast, insect and mammaliancells, preferably vertebrate cells such as those from a mouse, rat,monkey or human fibroblastic and colon cell lines. Yeast host cellsinclude YPH499, YPH500 and YPH501, which are generally available fromStratagene Cloning Systems, La Jolla, Calif. 92037, USA. Preferredmammalian host cells include Chinese hamster ovary (CHO) cells availablefrom the ATCC as CCL61, NIH Swiss mouse embryo cells NIH/3T3 availablefrom the ATCC as CRL 1658, monkey kidney-derived COS-1 cells availablefrom the ATCC as CRL 1650 and 293 cells, which are human embryonickidney cells. Preferred insect cells are Sf9 cells, which can betransfected with baculovirus expression vectors. An overview regardingthe choice of suitable host cells for expression can be found in, forexample, the textbook of Paulina Balbas and Argelia Lorence “Methods inMolecular Biology Recombinant Gene Expression, Reviews and Protocols,”Part One, Second Edition, ISBN 978-1-58829-262-9, and other literatureknown to the person of skill.

Transformation of appropriate cell hosts with a DNA construct of thepresent invention is accomplished by well known methods that typicallydepend on the type of vector used. With regard to transformation ofprokaryotic host cells, see, for example, Cohen et al (1972) Proc. Natl.Acad. Sci. USA 69, 2110, and Sambrook et al (1989) Molecular Cloning, ALaboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor,N.Y. Transformation of yeast cells is described in Sherman et al (1986)Methods In Yeast Genetics, A Laboratory Manual, Cold Spring Harbor, N.Y.The method of Beggs (1978) Nature 275, 104-109 is also useful. Withregard to vertebrate cells, reagents useful in transfecting such cells,for example calcium phosphate and DEAE-dextran or liposome formulations,are available from Stratagene Cloning Systems, or Life TechnologiesInc., Gaithersburg, Md. 20877, USA. Electroporation is also useful fortransforming and/or transfecting cells and is well known in the art fortransforming yeast cell, bacterial cells, insect cells and vertebratecells.

Successfully transformed cells, i.e. cells that contain a DNA constructof the present invention, can be identified by well known techniquessuch as PCR. Alternatively, the presence of the protein in thesupernatant can be detected using antibodies.

It will be appreciated that certain host cells of the invention areuseful in the preparation of the peptides of the invention, for examplebacterial, yeast and insect cells. However, other host cells may beuseful in certain therapeutic methods. For example, antigen-presentingcells, such as dendritic cells, may usefully be used to express thepeptides of the invention such that they may be loaded into appropriateMHC molecules. Thus, the current invention provides a host cellcomprising a nucleic acid or an expression vector according to theinvention.

In a preferred embodiment, the host cell is an antigen presenting cell,in particular a dendritic cell or antigen presenting cell. APCs loadedwith a recombinant fusion protein containing prostatic acid phosphatase(PAP) are currently under investigation for the treatment of prostatecancer (Sipuleucel-T) (Small E J et al 2006; Rini et al 2006).

A further aspect of the invention provides a method of producing apeptide or its variant, the method comprising culturing a host cell andisolating the peptide from the host cell or its culture medium.

In another embodiment the peptide, the nucleic acid or the expressionvector of the invention are used in medicine. For example, the peptideor its variant may be prepared for intravenous (i.v.) injection,sub-cutaneous (s.c.) injection, intradermal (i.d.) injection,intraperitoneal (i.p.) injection, intramuscular (i.m.) injection.Preferred methods of peptide injection include s.c., i.d., i.p., i.m.,and i.v. Preferred methods of DNA injection include i.d., i.m., s.c.,i.p. and i.v. Doses of e.g. between 50 μg and 1.5 mg, preferably 125 μgto 500 μg, of peptide or DNA may be given and will depend on therespective peptide or DNA. Doses of this range were successfully used inprevious trials (Brunsvig et al 2006; Staehler et al 2007).

Another aspect of the present invention includes an in vitro method forproducing activated T cells, the method comprising contacting T-cells invitro with antigen loaded human class I or II MHC molecules expressed onthe surface of a suitable antigen-presenting cell for a period of timesufficient to activate the T-cell in an antigen specific manner, whereinthe antigen is a peptide according to the invention. Preferably, asufficient amount of the antigen is used with an antigen-presentingcell.

In the case of a MHC class II epitope being used as an antigen, theT-cells are CD4-positive helper cells, preferably of T_(H1)-type. TheMHC class II molecules may be expressed on the surface of any suitablecell. Preferably the cell does not naturally express MHC class IImolecules (in which case the cell has been transfected in order toexpress such a molecule). Alternatively, if the cell naturally expressesMHC class II molecules, it is preferred that it is defective in theantigen-processing or antigen-presenting pathways. In this way, it ispossible for the cell expressing the MHC class II molecule to becompletely loaded with a chosen peptide antigen before activating theT-cell.

The antigen-presenting cell (or stimulator cell) typically has MHC classII molecules on its surface and preferably is itself substantiallyincapable of loading said MHC class II molecule with the selectedantigen. The MHC class II molecule may readily be loaded with theselected antigen in vitro.

Preferably, the mammalian cell lacks or has a reduced level or functionof the TAP peptide transporter. Suitable cells that lack the TAP peptidetransporter include T2, RMA-S and Drosophila cells. TAP is theTransporter associated with Antigen Processing.

The human peptide loading deficient cell line T2 is available from theAmerican Type Culture Collection, 12301 Parklawn Drive, Rockville, Md.20852, USA under Catalogue No CRL 1992; the Drosophila cell lineSchneider line 2 is available from the ATCC under Catalogue No CRL19863; the mouse RMA-S cell line is described in Karre et al. 1985.

Preferably, the host cell before transfection expresses substantially noMHC class I molecules. It is also preferred that the stimulator cellexpresses a molecule important for providing a co-stimulatory signal forT-cells such as any of B7.1, B7.2, ICAM-1 and LFA 3. The nucleic acidsequences of numerous MHC class II molecules and of the costimulatormolecules are publicly available from the GenBank and EMBL databases.

Similarly, when a MHC class I epitope is used as an antigen, the T cellsare CD8-positive CTLs.

If an antigen-presenting cell is transfected to express such an epitope,preferably the cell comprises an expression vector capable of expressinga peptide containing SEQ ID NO: 1 to SEQ ID NO: 3 or a variant aminoacid sequence thereof.

A number of other methods may be used for generating CTL in vitro. Forexample, the methods described in Peoples et al. (1995) and Kawakami etal (1992) use autologous tumor-infiltrating lymphocytes in thegeneration of CTL. Plebanski et al. (1995) makes use of autologousperipheral blood lymphocytes (PLBs) in the preparation of CTL. Jochmuset al. (1997) describes the production of autologous CTL by pulsingdendritic cells with peptide or polypeptide, or via infection withrecombinant virus. Hill et al. (1995) and Jerome et al. (1993) make useof B cells in the production of autologous CTL. In addition, macrophagespulsed with peptide or polypeptide, or infected with recombinant virus,may be used in the preparation of autologous CTL. S. Walter et al. 2003describe the in vitro priming of T cells by using artificial antigenpresenting cells (aAPCs), which is also a suitable way for generating Tcells against the peptide of choice. In this study, aAPCs were generatedby the coupling of preformed MHC:peptide complexes to the surface ofpolystyrene particles (microbeads) by biotin:streptavidin biochemistry.This system permits the exact control of the MHC density on aAPCs, whichallows to selectively elicit high- or low-avidity antigen-specific Tcell responses with high efficiency from blood samples. Apart fromMHC:peptide complexes, aAPCs should carry other proteins withco-stimulatory activity like anti-CD28 antibodies coupled to theirsurface. Furthermore such aAPC-based systems often require the additionof appropriate soluble factors, e.g. cytokines like interleukin-12.

Allogeneic cells may also be used in the preparation of T cells and amethod is described in detail in WO 97/26328, incorporated herein byreference. For example, in addition to Drosophila cells and T2 cells,other cells may be used to present antigens such as CHO cells,baculovirus-infected insect cells, bacteria, yeast, vaccinia-infectedtarget cells. In addition plant viruses may be used (see, for example,Porta et al. (1994)) which describes the development of cowpea mosaicvirus as a high-yielding system for the presentation of foreignpeptides.

The activated T-cells that are directed against the peptides of theinvention are useful in therapy. Thus, a further aspect of the inventionprovides activated T cells obtainable by the foregoing methods of theinvention. Activated T cells, which are produced by the above method,will selectively recognize a cell that aberrantly expresses apolypeptide that comprises an amino acid sequence of SEQ ID NO: 1 to SEQID NO: 3.

Preferably, the T-cell recognizes the cell by interacting through itsTCR with the HLA/peptide-complex (for example, binding). The T-cells areuseful in a method of killing target cells in a patient whose targetcells aberrantly express a polypeptide comprising an amino acid sequenceof the invention wherein the patient is administered an effective numberof the activated T-cells. The T-cells that are administered to thepatient may be derived from the patient and activated as described above(i.e. they are autologous T-cells). Alternatively, the T-cells are notfrom the patient but are from another individual. Of course, it ispreferred if the individual is a healthy individual. By “healthyindividual” the inventors mean that the individual is generally in goodhealth, preferably has a competent immune system and, more preferably,is not suffering from any disease which can be readily tested for, anddetected.

In vivo, the target cells for the CD4-positive T-cells according to thepresent invention can be cells of the tumor (which sometimes express MHCclass II) and/or stromal cells surrounding the tumor (tumor cells)(which sometimes also express MHC class II (Dengjel et al., 2006)).

The T-cells of the present invention may be used as active ingredientsof a therapeutic composition. Thus, the invention also provides a methodof killing target cells in a patient whose target cells aberrantlyexpress a polypeptide comprising an amino acid sequence of theinvention, the method comprising administering to the patient aneffective number of T-cells as defined above.

By “aberrantly expressed” the inventors also mean that the polypeptideis over-expressed compared to normal levels of expression or that thegene is silent in the tissue from which the tumor is derived but in thetumor it is expressed. By “over-expressed” the inventors mean that thepolypeptide is present at a level at least 1.2-fold of that present innormal tissue; preferably at least 2-fold, and more preferably at least5-fold or 10-fold the level present in normal tissue.

T-cells may be obtained by methods known in the art, e.g. thosedescribed above. Protocols for this so-called adoptive transfer ofT-cells are well known in the art and can be found, e.g. in (Rosenberget al., 1987; Rosenberg et al., 1988; Dudley et al., 2002; Yee et al.,2002; Dudley et al., 2005); reviewed in (Gattinoni et al., 2006) and(Morgan et al., 2006).

Any molecule of the invention, i.e. the peptide, nucleic acid,expression vector, cell, activated CTL, T-cell receptor or the nucleicacid encoding it is useful for the treatment of disorders, characterizedby cells escaping an immune response. Therefore any molecule of thepresent invention may be used as medicament or in the manufacture of amedicament. The molecule may be used by itself or combined with othermolecule(s) of the invention or (a) known molecule(s).

Preferably, the medicament of the present invention is a vaccine. It maybe administered directly into the patient, into the affected organ orsystemically i.d., i.m., s.c., i.p. and i.v., or applied ex vivo tocells derived from the patient or a human cell line which aresubsequently administered to the patient, or used in vitro to select asubpopulation of immune cells derived from the patient, which are thenre-administered to the patient. If the nucleic acid is administered tocells in vitro, it may be useful for the cells to be transfected so asto co-express immune-stimulating cytokines, such as interleukin-2 Thepeptide may be substantially pure, or combined with animmune-stimulating adjuvant (see below) or used in combination withimmune-stimulatory cytokines, or be administered with a suitabledelivery system, for example liposomes. The peptide may also beconjugated to a suitable carrier such as keyhole limpet haemocyanin(KLH) or mannan (see WO 95/18145 and Longenecker et al. (1993)). Thepeptide may also be tagged, may be a fusion protein, or may be a hybridmolecule. The peptides whose sequence is given in the present inventionare expected to stimulate CD4 or CD8 T-cells. However, stimulation ofCD8 CTLs is more efficient in the presence of help provided by CD4T-helper cells. Thus, for MHC Class I epitopes that stimulate CD8 CTL,the fusion partner or sections of a hybrid molecule suitably provideepitopes that stimulate CD4-positive T cells. CD4- and CD8-stimulatingepitopes are well known in the art and include those identified in thepresent invention.

In one aspect, the vaccine comprises at least one peptide having theamino acid sequence set forth in SEQ ID NO:1, 2 or 3 and at least oneadditional peptide, preferably two to 50, more preferably two to 25,even more preferably two to 15 and most preferably two, three, four,five, six, seven, eight, nine, ten, eleven, twelve or thirteen peptides.The peptide(s) may be derived from one or more specific TAAs and maybind to MHC class I and/or class II molecules. Preferably the at leastone additional peptide has the amino acid sequence set forth in SEQ IDNO: 4 to 24.

The polynucleotide may be substantially pure, or contained in a suitablevector or delivery system. The nucleic acid may be DNA, cDNA, PNA, CNA,RNA or a combination thereof. Methods for designing and introducing sucha nucleic acid are well known in the art. An overview is provided bye.g. Pascolo S. 2006; Stan R. 2006, or A Mandavi 2006. Polynucleotidevaccines are easy to prepare, but the mode of action of these vectors ininducing an immune response is not fully understood. Suitable vectorsand delivery systems include viral DNA and/or RNA, such as systems basedon adenovirus, vaccinia virus, retroviruses, herpes virus,adeno-associated virus or hybrids containing elements of more than onevirus. Non-viral delivery systems include cationic lipids and cationicpolymers and are well known in the art of DNA delivery. Physicaldelivery, such as via a “gene-gun,” may also be used. The peptide orpeptides encoded by the nucleic acid may be a fusion protein, forexample with an epitope that stimulates T cells for the respectiveopposite CDR as noted above.

The medicament of the invention may also include one or more adjuvants.Adjuvants are substances that non-specifically enhance or potentiate theimmune response (e.g., immune responses mediated by CTLs and helper-T(T_(H)) cells to an antigen, and would thus be considered useful in themedicament of the present invention. Suitable adjuvants include, but arenot limited to, 1018 ISS, aluminium salts, AMPLIVAX®, AS15, BCG,CP-870,893, CpG7909, CyaA, dSLIM, flagellin or TLR5 ligands derived fromflagellin, FLT3 ligand, GM-CSF, IC30, IC31, Imiquimod (ALDARA®), ImuFactIMP321, Interleukins as IL-2, IL-13, IL-21, Interferon-alpha or -beta,or pegylated derivatives thereof, IS Patch, ISS, ISCOMATRIX®, ISCOMs,JUVIMMUNE®, LIPOVAC®, MALP2, MF59, monophosphoryl lipid A, MONTANIDE®IMS 1312, MONTANIDE® ISA 206, MONTANIDE® ISA 50V, MONTANIDE® ISA-51,water-in-oil and oil-in-water emulsions, OK-432, OM-174, OM-197-MP-EC,ONTAK®, OspA, PepTel® vector system, PLG and dextran microparticles,resiquimod, SRL172, Virosomes and other Virus-like particles, YF-17D,VEGF trap, R848, beta-glucan, Pam3Cys, Aquila's QS21 STIMULON®, which isderived from saponin, mycobacterial extracts and synthetic bacterialcell wall mimics, and other proprietary adjuvants such as Ribi's Detox,Quil, or Superfos. Adjuvants such as Freund's or GM-CSF are preferred.Several immunological adjuvants (e.g., MF59) specific for dendriticcells and their preparation have been described previously (Dupuis M etal. 1998; Allison 1998). Also cytokines may be used. Several cytokineshave been directly linked to influencing dendritic cell migration tolymphoid tissues (e.g., TNF-α), accelerating the maturation of dendriticcells into efficient antigen-presenting cells for T-lymphocytes (e.g.,GM-CSF, IL-1 and IL-4) (U.S. Pat. No. 5,849,589, specificallyincorporated herein by reference in its entirety) and acting asimmunoadjuvants (e.g., IL-12, IL-15, IL-23, IL-7, IFN-alpha. IFN-beta)(Gabrilovich et al. 1996).

CpG immunostimulatory oligonucleotides have also been reported toenhance the effects of adjuvants in a vaccine setting. Without beingbound by theory, CpG oligonucleotides act by activating the innate(non-adaptive) immune system via Toll-like receptors (TLR), mainly TLR9.CpG triggered TLR9 activation enhances antigen-specific humoral andcellular responses to a wide variety of antigens, including peptide orprotein antigens, live or killed viruses, dendritic cell vaccines,autologous cellular vaccines and polysaccharide conjugates in bothprophylactic and therapeutic vaccines. More importantly it enhancesdendritic cell maturation and differentiation, resulting in enhancedactivation of T_(H1) cells and strong cytotoxic T-lymphocyte (CTL)generation, even in the absence of CD4 T cell help. The T_(H1) biasinduced by TLR9 stimulation is maintained even in the presence ofvaccine adjuvants such as alum or incomplete Freund's adjuvant (IFA)that normally promote a T_(H2) bias. CpG oligonucleotides show evengreater adjuvant activity when formulated or co-administered with otheradjuvants or in formulations such as microparticles, nanoparticles,lipid emulsions or similar formulations, which are especially necessaryfor inducing a strong response when the antigen is relatively weak. Theyalso accelerate the immune response and enable the antigen doses to bereduced by approximately two orders of magnitude, with comparableantibody responses to the full-dose vaccine without CpG in someexperiments (Krieg et al. 2006). U.S. Pat. No. 6,406,705 B1 describesthe combined use of CpG oligonucleotides, non-nucleic acid adjuvants andan antigen to induce an antigen-specific immune response. A CpG TLR9antagonist is dSLIM (double Stem Loop Immunomodulator) by Mologen(Berlin, Germany), which is a preferred component of the pharmaceuticalcomposition of the present invention. Other TLR binding molecules suchas RNA binding TLR 7, TLR 8 and/or TLR 9 may also be used.

Other examples for useful adjuvants include, but are not limited tochemically modified CpGs (e.g. CpR, Idera), dsRNA analogues such asPoly(I:C) and AMPLIGEN®, non-CpG bacterial DNA or RNA as well asimmunoactive small molecules and antibodies such as cyclophosphamide,sunitinib, Bevacizumab, CELEBREX®, NCX-4016, sildenafil, tadalafil,vardenafil, sorafenib, temozolomide, temsirolimus, XL-999, CP-547632,pazopanib, VEGF Trap, ZD2171, AZD2171, anti-CTLA4 and SC58175, which mayact therapeutically and/or as an adjuvant. The amounts andconcentrations of adjuvants and additives useful in the context of thepresent invention can readily be determined by the skilled artisanwithout undue experimentation. Preferred adjuvants are dSLIM,Interferon-alpha, -beta, CpG7909, IC31, ALDARA® (Imiquimod), PeviTer,RNA, tadalafil, temozolomide, and JUVIMMUNE®.

The present invention provides a medicament that useful in treatingcancer, in particular glioma and brain cancer, breast cancer, prostatecancer, esophagus cancer, colorectal cancer, renal cancer, pancreaticcancer, squamous cell carcinomas and keratinocytic neoplasms of theskin, leukemia, lung cancer, ovarian cancer, and melanoma.

The present invention includes a kit comprising: (a) a container thatcontains a pharmaceutical composition as described above, in solution orin lyophilized form; (b) optionally a second container containing adiluent or reconstituting solution for the lyophilized formulation; and(c) optionally, instructions for (i) use of the solution or (ii)reconstitution and/or use of the lyophilized formulation.

The kit may further comprise one or more of (iii) a buffer, (iv) adiluent, (v) a filter, (vi) a needle, or (v) a syringe. The container ispreferably a bottle, a vial, a syringe or test tube; and it may be amulti-use container. The pharmaceutical composition is preferablylyophilized.

Kits of the present invention preferably comprise a lyophilizedformulation of the present invention in a suitable container andinstructions for its reconstitution and/or use. Suitable containersinclude, for example, bottles, vials (e.g. dual chamber vials), syringes(such as dual chamber syringes) and test tubes. The container may beformed from a variety of materials such as glass or plastic. Preferablythe kit and/or container contains instructions on or associated with thecontainer that indicates directions for reconstitution and/or use. Forexample, the label may indicate that the lyophilized formulation is tobe reconstituted to peptide concentrations as described herein. Thelabel may further indicate that the formulation is useful or intendedfor subcutaneous administration.

The container holding the formulation may be a multi-use vial, whichallows for repeat administrations (e.g., from 2 to 6 administrations) ofthe reconstituted formulation. The kit may further comprise a secondcontainer comprising a suitable diluent (e.g., sodium bicarbonatesolution).

Upon mixing of the diluent and the lyophilized formulation, the finalpeptide concentration in the reconstituted formulation is preferably atleast 0.15 mg/mL/peptide (=75 μg) and preferably not more than 3mg/mL/peptide (=1500 μg). The kit may further include other materialsdesirable from a commercial and user standpoint, including otherbuffers, diluents, filters, needles, syringes, and package inserts withinstructions for use.

Kits of the present invention may have a single container that containsthe formulation of the pharmaceutical compositions according to thepresent invention with or without other components (e.g., othercompounds or pharmaceutical compositions of these other compounds) ormay have distinct container for each component.

Preferably, kits of the invention include a formulation of the inventionpackaged for use in combination with the co-administration of a secondcompound (such as adjuvants (e.g. GM-CSF), a chemotherapeutic agent, anatural product, a hormone or antagonist, a anti-angiogenesis agent orinhibitor, a apoptosis-inducing agent or a chelator) or a pharmaceuticalcomposition thereof. The components of the kit may be pre-complexed oreach component may be in a separate distinct container prior toadministration to a patient. The components of the kit may be providedin one or more liquid solutions, preferably, an aqueous solution, morepreferably, a sterile aqueous solution. The components of the kit mayalso be provided as solids, which may be converted into liquids byaddition of suitable solvents, which are preferably provided in anotherdistinct container.

The container of a therapeutic kit may be a vial, test tube, flask,bottle, syringe, or any other means of enclosing a solid or liquid.Usually, when there is more than one component, the kit will contain asecond vial or other container, which allows for separate dosing. Thekit may also contain another container for a pharmaceutically acceptableliquid. Preferably, a therapeutic kit will contain an apparatus (e.g.,one or more needles, syringes, eye droppers, pipette, etc.), whichenables administration of the agents of the invention that arecomponents of the present kit.

The present formulation is one that is suitable for administration ofthe peptides by any acceptable route such as oral (enteral), nasal,ophthalmic, subcutaneous, intradermal, intramuscular, intravenous ortransdermal. Preferably the administration is s.c., and most preferably,i.d. Administration may be by infusion pump.

Regarding the sequencing listing, SEQ ID NO: 1 to SEQ ID NO: 3 show thesequences of the tumor associated peptide of the present inventionderived from survivin.

SEQ ID NO: 4 to SEQ ID NO: 13 and SEQ ID NO: 24 show the sequences ofother tumor associated peptides used in the present invention. SEQ IDNO: 14 shows the sequences of the peptide of HBV. SEQ ID NO: 15 to SEQID NO: 23 show the sequences of other tumor associated peptides used inthe present invention. SEQ ID NO: 25 to SEQ ID NO: 27 show the sequencesof the associated peptides of Wang et al. (WO 2007/036638). SEQ ID NO:28 to SEQ ID NO: 33 show the sequences of tumor associated peptides ofPiesche. SEQ ID NO: 34 to SEQ ID NO: 63 show the sequences of thePeptides as designed in Example 3. SEQ ID NO: 64 and SEQ ID NO: 65 showthe sequences of the Peptides as used in Example 4.

The present invention will now be described in the following examplesthat describe preferred embodiments thereof, nevertheless, without beinglimited thereto. For the purposes of the present invention, allreferences as cited herein are incorporated by reference in theirentireties.

EXAMPLES Example 1 Identification of Tumor Associated Peptides Presentedon Cell Surface

Tissue Samples

Patients' tumor and healthy tissues were provided by Hôpital CantonalUniversitaire de Genève (Medical Oncology Laboratory of TumorImmunology) and Neurochirurgische Universitäts-Klinik Heidelberg(Molekularbiologisches Labor). Written informed consents of all patientshad been given before surgery. Tissues were shock-frozen in liquidnitrogen immediately after surgery and stored until isolation ofpeptides at −80° C.

Isolation of HLA Peptides from Tissue Samples

HLA peptide pools from shock-frozen tissue samples were obtained byimmune precipitation from solid tissues according to a slightly modifiedprotocol (Falk, K. et al 1991; Seeger, F. H. et al. T 1999) using theHLA-A*02-specific antibody BB7.2 or the HLA-A, -B, -C-specific antibodyW6/32, CNBr-activated sepharose, acid treatment, and ultrafiltration.

Method Two:

The HLA peptide pools as obtained were separated according to theirhydrophobicity by reversed-phase chromatography (Acquity UPLC system,Waters) and the eluting peptides were analyzed in an LTQ-Orbitrap hybridmass spectrometer (ThermoElectron) equipped with an ESI source. Peptidepools were loaded directly onto the analytical fused-silicamicro-capillary column (75 μm i.d.×250 mm) packed with 1.7 μm C18reversed-phase material (Waters) applying a flow rate of 400 nL perminute. Subsequently, the peptides were separated using a two-step 180minute-binary gradient from 10% to 33% B at flow rates of 300 nL perminute. The gradient was composed of Solvent A (0.1% formic acid inwater) and solvent B (0.1% formic acid in acetonitrile). A gold coatedglass capillary (PicoTip, New Objective) was used for introduction intothe micro-ESI source. The LTQ-Orbitrap mass spectrometer was operated inthe data-dependent mode using a TOP5 strategy. In brief, a scan cyclewas initiated with a full scan of high mass accuracy in the orbitrap(R=30 000), which was followed by MS/MS scans also in the orbitrap(R=7500) on the 5 most abundant precursor ions with dynamic exclusion ofpreviously selected ions. Tandem mass spectra were interpreted bySEQUEST and additional manual control. The identified peptide sequencewas assured by comparison of the generated natural peptide fragmentationpattern with the fragmentation pattern of a synthetic sequence-identicalreference peptide. FIG. 1 shows an exemplary spectrum obtained fromtumor tissue for the MHC class I associated peptide NCAN-001.

Example 2 Expression Profiling of Genes Encoding the Peptides of theInvention

Not all peptides identified as being presented on the surface of tumorcells by MHC molecules are suitable for immunotherapy, because themajority of these peptides are derived from normal cellular proteinsexpressed by many cell types. Only few of these peptides aretumor-associated and likely able to induce T cells with a highspecificity of recognition for the tumor from which they were derived.To identify such peptides and minimize the risk for autoimmunity inducedby vaccination the inventors focused on those peptides that are derivedfrom proteins that are over-expressed on tumor cells compared to themajority of normal tissues.

The “ideal” peptide will be derived from a protein that is unique to thetumor and not present in any other tissue. To identify peptides that arederived from genes with an expression profile similar to the “ideal”peptide, the identified peptides were assigned to the proteins andgenes, respectively, from which they were derived and expressionprofiles of these genes were generated.

RNA Sources and Preparation

Surgically removed tissue specimens were provided by two differentclinical sites (see Example 1) after written informed consent had beenobtained from each patient. Tumor tissue specimens were snap-frozen inliquid nitrogen immediately after surgery and later homogenized withmortar and pestle under liquid nitrogen. Total RNA was prepared fromthese samples using TRIzol (Invitrogen, Karlsruhe, Germany) followed bya cleanup with RNEASY® (QIAGEN, Hilden, Germany); both methods wereperformed according to the manufacturer's protocol.

Total RNA from healthy human tissues was obtained commercially (Ambion,Huntingdon, UK; Clontech, Heidelberg, Germany; Stratagene, Amsterdam,Netherlands; BioChain, Hayward, Calif., USA). The RNA from severalindividuals (between 2 and 123 individuals) was mixed such that RNA fromeach individual was equally weighted. Leukocytes were isolated fromblood samples of 4 healthy volunteers.

Quality and quantity of all RNA samples were assessed on an Agilent 2100Bioanalyzer (Agilent, Waldbronn, Germany) using the RNA 6000 PicoLabChip Kit (Agilent).

Microarray Experiments

Gene expression analysis of all tumor and normal tissue RNA samples wasperformed by Affymetrix Human Genome (HG) U133A or HG-U133 Plus 2.0oligonucleotide microarrays (Affymetrix, Santa Clara, Calif., USA). Allsteps were carried out according to the Affymetrix manual. Briefly,double-stranded cDNA was synthesized from 5-8 μg of total RNA, usingSuperScript RTII (Invitrogen) and the oligo-dT-T7 primer (MWG Biotech,Ebersberg, Germany) as described in the manual. In vitro transcriptionwas performed with the BioArray High Yield RNA Transcript Labelling Kit(ENZO Diagnostics, Inc., Farmingdale, N.Y., USA) for the U133A arrays orwith the GeneChip IVT Labelling Kit (Affymetrix) for the U133 Plus 2.0arrays, followed by cRNA fragmentation, hybridization, and staining withstreptavidin-phycoerythrin and biotinylated anti-streptavidin antibody(Molecular Probes, Leiden, Netherlands). Images were scanned with theAgilent 2500A GeneArray Scanner (U133A) or the Affymetrix Gene-ChipScanner 3000 (U133 Plus 2.0), and data were analyzed with the GCOSsoftware (Affymetrix), using default settings for all parameters. Fornormalization, 100 housekeeping genes provided by Affymetrix were used.Relative expression values were calculated from the signal log ratiosgiven by the software and the normal sample was arbitrarily set to 1.0.

The expression profile of the source gene NCAN of the peptide NCAN-001of the present invention shows a high expression in glioblastoma tumortissue whereas the gene is not expressed or expressed at very low levelsin normal tissues (FIG. 2).

Example 3 HLA-DR Motif Peptides from Survivin (Swissprot: O15392)

Epitope Prediction: Prediction of potential HLA-DR ligands was carriedout using the database SYFPEITHI. Briefly, the sequence of survivin wasscreened against a matrix pattern which evaluates every amino acidwithin the nonamer core sequence of 15mer peptides fitting therespective HLA-DR motif. Anchor residues are given values of up to 10;other residues values up to 3, reflecting amino acid preferences forcertain positions within the peptide. The theoretical maximum score fora candidate peptide varies from 28 to 43; scores for abundant naturalligands are typically above 20.

TLGEFLKLDRERAKN (SEQ ID NO: 1) (or truncated versions) appears among thetop scoring peptides in 5 of 6 predictions.

DRB1*01 (maximal theoretical score 43)  58 FFCFKELEGWEPDDD(SEO ID NO: 34) 36  98 LGEFLKLDRERAKNK (SEQ ID NO: 35) 28  22FKNWPFLEGCACTPE (SEQ ID NO: 36) 28DRB1*03 (maximal theoretical score 40)  99 GEFLKLDRERAKNKI(SEQ ID NO: 37) 29  10 WQPFLKDHRISTFKN (SEQ ID NO: 38) 26   3APTLPPAWQPFLKDH (SEQ ID NO: 39) 25DRB1*04 (maximal theoretical score 28)  98 LGEFLKLDRERAKNK(SEQ ID NO: 40) 28  10 WQPFLKDHRISTFKN (SEQ ID NO: 41) 28   3APTLPPAWQPFLKDH (SEQ ID NO: 42) 26DRB1*07 (maximal theoretical score 34) 121 KKEFEETAEKVRRAI(SEQ ID NO: 43) 24 128 AEKVRRAIEQLAAMD (SEQ ID NO: 44) 24   3APTLPPAWQPFLKDH (SEQ ID NO: 45) 22  16 DHRISTFKNWPFLEG (SEQ ID NO: 46)20  28 LEGCACTPERMAEAG (SEQ ID NO: 47) 18  40 EAGFIHCPTENEPDL(SEQ ID NO: 48) 18  93 FEELTLGEFLKLDRE (SEQ ID NO: 49) 16 103KLDRERAKNKIAKET (SEQ ID NO: 50) 16DRB1*11 (maximal theoretical score 38)  98 LGEFLKLDRERAKNK(SEQ ID NO: 51) 32  83 GCAFLSVKKQFEELT (SEQ ID NO: 52) 24  58FFCFKELEGWEPDDD (SEQ ID NO: 53) 22DRB1*15 (maximal theoretical score 34)  95 ELTLGEFLKLDRERA(SEQ ID NO: 54) 30  19 ISTFKNWPFLEGCAC (SEQ ID NO: 55) 28  55AQCFFCFKELEGWEP (SEQ ID NO: 56) 28Steps Leading to the Decision about the Sequence1. For each peptide, a 9mer core sequence is necessary for HLA-DRbinding. Predicted core sequences:

DRB1*01 FLKLDRERA (SEQ ID NO: 57) DRB1*03 LKLDRERAK (SEQ ID NO: 58)DRB1*04 FLKLDRERA (SEQ ID NO: 59) DRB1*11 FLKLDRERA (SEQ ID NO: 60)DRB1*15 LGEFLKLDR (SEQ ID NO: 61)2. Combine core sequences to obtain one promiscuous core sequence:

Combined: LGEFLKLDRERAK (SEQ ID NO: 62)3. Add flanking sequences to a final length of 15 amino acids:

Final: TLGEFLKLDRERAK (SEQ ID NO: 63)

Example 4 Clinical Study

A clinical study was conducted to confirm the immunogenicity of thepeptide with the SEQ ID NO: 1. The primary study objective was theinvestigation of the PSA (prostate-specific antigen)-based response(PSA-R) to the subcutaneous administration of a prostate-specificpeptide panel (vaccination therapy) in patients with biochemical relapseafter radical prostatectomy without detection of manifest metastaticlesions.

The secondary study objective was the investigation of the tolerabilityand feasibility of administering vaccination therapy in patients withprostate carcinoma with special consideration of immunological phenomenain terms of a T cell response.

The study was designed as a prospective, randomized Phase I/II study forthe indication of “biochemical relapse after radical prostatectomywithout detection of manifest metastatic lesions.”

Study Population

As part of this Phase I/II study, an attempt was made to induce PSAregression as an indicator of cessation of tumor growth by means ofvaccination with a prostate-specific peptide panel in HLA-A*02⁺ patientswith biochemical relapse after radical prostatectomy. A combination ofprostate-specific peptides was administered subcutaneously withevaluation of the extent of the respective immune response in thecontext of various administration forms of the antigenic structures.

In contrast to previous vaccination studies, the planned study targetedthe treatment of patients with a small tumor burden not yet detectableby imaging procedures. The patients were all immunized in the same wayusing known prostate-specific antigenic structures to enhance the immuneresponse to the malignantly transformed cells. —Nineteen patients weretreated.

TABLE 7 Study population Total % Median Range Age 19 63 55-77 Priorneo-/adjuvant treatment None 11 58 Radiation 3 16 Intermittent HormonalTherapy 2 11 Rad. + Int. Horm. Therapy 2 11 Rad. + Chemotherapy 1 5 TNMat RPX T2a-c R0 6 32 T3a-c R0 6 32 T2a-c R1 3 16 T3a-c R1 3 16 T3aN2 R01 5 Gleason score 5-7 10 53 8-10 3 16 unknown 6 32 RPX prior tovaccination in 41  9-124 months First relapse post OP in months 14  1-90PSA at vaccination start 0.76 0.14-10.8

Treatment Schedule

After rule-out of manifest metastatic lesions using computed tomographyand skeletal scintigraphy, the prostate-specific peptide vaccine wassubcutaneously administered according to the different administrationforms to patients with detected PSA relapse after prior radicalprostatectomy (PSA increase in terms of a 50% elevated value during twomeasurements at least 14 days apart). The vaccine was administered 8× ondays 0, 7, 14, 28, 42, and 56 (approximately 100 micrograms per peptideand injection each time). After each vaccination treatment and again onday 70, PSA was measured to evaluate the therapeutic response.

If a tumor response (complete remission [PSA-CR], partial remission[PSA-PR], or stable clinical course [no change, PSA-NC]) is detected,the patient received the vaccine once a month as maintenance therapyaccording to the selected administration form. The patient's response tovaccination therapy was evaluated in detail as follows:

Complete remission (PSA-CR): Normalization of an initially elevated PSAlevel, confirmed by measurement after an interval of at least 4 weeks.Normalization is defined as a PSA nadir of <0.2 ng/ml, which would beexpected after radical prostatectomy with complete tumor or prostateextirpation.

Partial remission: a) PSA-PR<80% (Reduction in an initially elevated PSAlevel by 80%, confirmed by measurement after an interval of at least 4weeks); and b) PSA-PR≦50% (Reduction in an initially elevated PSA levelby 50%, confirmed by measurement after an interval of at least 4 weeks.)

Stable disease (PSA-SD): No significant change over a period of at leastfour weeks. This includes stabilization and a reduction of less than 50%and an increase of less than 10%, confirmed by measurement after aninterval of at least 4 weeks.

Progression (PSA-PD): Increase in the PSA level by more than 10%. In theevent of PSA progression, the study was terminated.

After enrollment of the patients in the study, the epitope-specificvaccine was used; the proteins specifically expressed in prostaticepithelial cells (e.g., PSMA/PSCA) were taken into account. In additionto investigating the general efficacy of the administered vaccine withrespect to monitoring the growth of residual tumor fractions asevaluated by PSA monitoring, this study investigated the effects ofvarious vaccination methods with respect to efficient modulation of theimmune system. In addition to simple subcutaneous administration of thepeptides according to the invention alone, various combinations withadjuvants were also used. The vaccine included a combination of at least6 peptides derived from PSA, PSCA, PSMA, Survivin, TRP-P8 and Prostein,respectively. A peptide derived from influenza MP was used as a positivecontrol. Peptides derived from PSMA and Survivin were used at T helperepitopes. In particular, depot and adjuvant activity for peptidevaccines of MONTANIDE® (a formulation of the classical incompleteFreund's adjuvant suitable for use in humans), which has recently beendescribed very favorably, was used. For this purpose, 500 μl of thepeptide solution was mixed with 500 μl of MONTANIDE® and administered.Thereby, a water-in-oil emulsion is built that slowly releases theantigen contained in the aqueous phase over weeks. The physicalstability of the emulsion is very high, as at 4° C. it can be stored formore than 3 months without significant phase separation. The depotfunction of MONTANIDE® has been exploited in several vaccination trialswith good results (Okat et al., 2004).

One study arm investigated the efficacy of vaccination duringconcomitant stimulation of the immune system by growth factors, GM-CSF,Leukine® solution for injection. GM-CSF is a very commonly used adjuvantin peptide vaccination trials with several thereof reporting enhancedclinical and T-cell responses. Initially, GM-CSF is a dendritic cellrecruitment and differentiation factor that is thought to enhance thenumber of dendritic cell at the vaccines' injection site. AlthoughGM-CSF does not by itself activate antigen presenting cells as dendriticcells and macrophages an indirect activation in vivo has been reported(Molenkamp et al., 2005).

Another study arm investigated the efficacy of vaccination duringconcomitant activation of dendritic cells by epicutaneous use ofimiquimod. Imiquimod was administered as a 5% ointment (ALDARA®). It hasa strong immunostimulatory via its effect on TLR7 positive cells (e.g.plasmacytoid DCs, Langerhans cells, dermal DCs), activates theMyD88-dependent pathway. Activated APCs release T-cell stimulating andinflammatory cytokines, upregulate costimulation and migrate to draininglymph nodes. The potential of iniquimod to enhance peptide-induced CTLresponse by mixing the antigens into the ointment or by application ofALDARA® over the s.c. or i.d. injection site for the antigens has beendemonstrated in animal models.

Another study arm investigated the efficacy of vaccination duringconcomitant activation of dendritic cells by mixing them withprotamine-stabilized mRNA encoding mucin-1 to activate TLR 7/8. mRNAshows a broad activation of mouse and human immune cell populations. Thepresence of the poly-basic protein protamine in the formulationincreases the half-life of the mRNA and induces the formation ofpotentially depot-forming particles. This adjuvant may therefore combinedepot-forming and APC-activating properties.

In summary, the administration forms of the vaccine included thefollowing approaches:

a) Subcutaneous administration of the peptide vaccine emulsified inMONTANIDE®;

b) Subcutaneous administration of the peptide vaccine emulsified in 500μl of MONTANIDE® in combination with topical administration of 225 μl ofGM-CSF with the objective of achieving a stronger immune responsetriggered by concomitant administration of growth factors;

c) Subcutaneous administration of the peptide vaccine emulsified in 500μl of MONTANIDE® in combination with local hyperthermia, the lattergiven with the objective of achieving a thermally induced strongerimmune response;

d) Subcutaneous administration of the peptide vaccine emulsified in 500μl of MONTANIDE® in combination with epicutaneous imiquimod in order toactivate dendritic cells via TLR 7;

e) Subcutaneous administration of the peptide vaccine emulsified in 500μl of MONTANIDE® together with 55 μA of mucin-1 mRNA/protamine toactivate dendritic cells via TLR 7/8.

Schedule

The entire duration of the study was 3 years. Prostate-specific peptidevaccines were administered to patients on days 0, 7, 14, 28, 42, and 56.In patients with stable disease or an objective tumor response (PSA-CRor PSA-PR), the vaccinations were administered once a month i.d. untildetectable progression occurs. On the basis of the experience availablethus far, peptide injections are tolerated without significant adversereactions. Because the response to vaccination therapy was evaluatedsolely serologically on the basis of the PSA measurement, a test wasperformed at the start of the study to determine whether theadministered vaccine interferes with PSA measurement in vitro, whichcould simulate a clinical response. On days 0, 7, 14, 28, 42, 56, and70, blood samples was taken for laboratory tests, PSA levels,differential blood count, FACS analysis, and cytokines. If treatment iscontinued past day 70, 6-week PSA monitoring was performed to detecttreatment failure in a timely manner.

Treatment was ended if documented progression of the disease occurred interms of a continuous PSA elevation.

Beginning on day 84, immunization therapy was continued at 4-weekintervals until documented progression or up to day 420 (15 months).Decisions regarding continuation of therapy (in successful cases)outside of this study were made on a case-by-case basis. Unexpectedadverse reactions did not occur in this study.

The laboratory tests included coagulation, electrolytes, LDH, β2-M, CK,hepatic enzymes, bilirubin, creatinine, uric acid, total protein,coagulation, CRP, differential blood count with smear, PSA level,cytokines, FACS, ELISPOT®.

Analysis of the cutaneous reaction to defined bacterial and fungalantigens (48-72 hours after administration, delayed typehypersensitivity (DTH), T cell-mediated, served as an analysis of thepatient's cellular immune system before the start of the study).

The peptides required for the study (nona-peptides) were manufactured inthe laboratory of PD Dr. Stefan Stevanovic in the department of Prof.H.-G. Rammensee. These peptides were purified by HPLC and analyzed bymass spectrometry. The purity of the peptides can also be checked byHPLC, mass spectrometry, and Edman sequencing. Using these methods,purity of up to 98% can be documented (which must be regarded as themaximum according to the current state of the methods). The synthesizedpeptides was dissolved in DMSO (CryoSure, WAK Chemie Medical GmbH; 10mg/ml), diluted to 1:10 in Ampuwa (Fresenius Kabi), and aliquoted understerile conditions.

Clinical Response

In two patients PET-CT scan could reveal local recurrence after localtumor was detected by continuous digital rectal examination. In theremaining 17 patients the location of disease activity could not beverified at study termination.

Repeated laboratory evaluation of differential blood count or extensiveclinical chemistry did not reveal any abnormalities nor changes duringthe study.

Of the 19 patients, 16 patients reacted to the Survivin II peptide(IFN-g ELISPOT, +/−ICS) according to SEQ ID NO: 1. Among them were 12patients with induction of an anti-survivin T-cell response uponvaccination, 2 with pre-existing anti-Survivin T cells and 2 patients ofwhom it was not determined, whether pre-existing anti-Survivin T cellswere abundant.

Biochemical Response

Complete response was considered as a non-detectable PSA value accordingto the lowest value detected after initially elevated PSA. Themeasurement had to be confirmed after an interval of at least fourweeks. A PR>80% and >50% had to be reevaluated after four weeksaccordingly. A PSA within the range of less than 50% decrease or lessthan 10% increase reflected stable disease if at least confirmed afterfour weeks. Progressive disease was considered any increase of more than10% of PSA at treatment start.

Biochemical response in patients who terminated the study was followeduntil they received further treatment with local radiation orantihormonal therapy. 19 patients consented to participate and the datawas analyzed with the longest follow-up lasting about 3.75 years.

PSA Stability and DT Increase

PSA values of two patients (10.2%) exhibited stability according to theabove mentioned criteria of biochemical response which state that norise of the PSA value greater than 10% at treatment start had occurredat study end (FIG. 6, Tables 8, 9, and 10). Follow up in those two caseswas conducted 14 and 16 months after the last vaccine application.Average duration of stability was 24 months (28 and 31) at data cut-offwith an average of 18 vaccinations (14 and 20) applied.

Out of these two patients, one patient showed partial response>50% for aperiod of 9 months, followed by a period of slow PSA rise with adoubling time of 20.5 compared to 9.8 months prior vaccination. InitialPSA relapse started 18 months post surgery for a pT2pN0 Gleason 5 tumor.

At data analysis, Patient 8 exhibited stable disease since the beginningof the vaccination program. Patients stopped treatment due to anallergic reaction after 10 months and the 14^(th) vaccination. Thepatient had an unfavorable pT3b Gleason 3+4 situation with a PSA nadirafter radical prostatectomy not below 0.6 ng/ml and PSA progressionwithout timely delay after initial decline postoperatively. Doublingtime slowed from 6.6 months to 148 months.

These two patients received dermal Imiquimod at the application site ateach peptide vaccination (FIGS. 9, 10, and 11, Table 13).

PSA DT Increase without PSA Stability

PSA DT of Patient 11 was increased from 1.5 to 10.1 months during sixmonths in the study. Since the patient started with a PSA of 10.8 ng/mland progressed to 17.8 ng/ml, the patient terminated the study toreceive antiandrogen monotherapy without any malignant lesionsvisualized in PET-CT. The patient received ALDARA® as adjuvant.

Patient 16 started into vaccine treatment plus Mucin-1-mRNA/protaminewith a doubling time of 6.1 months. PSA velocity declined into a halflife time of 2.7 months for five months followed by a statisticallycalculated rise of PSA DT of 14.4 months which is continuing 16 monthsafter treatment start. With an initial PSA of 0.29 ng/ml, he dropped to0.19 ng/ml during the first 5 months on study treatment, rose to 0.4ng/ml within the following 8 months and terminated the study perprotocol with 0.41 ng/ml 19 months after treatment start (FIG. 7 Table 8and 10).

PSA Progression

Patient 5 progressed during the study according to the estimated PSAdoubling time before vaccination. However, the patient experienced a PSAdecline with a half-time life of 20.2 months after treatment end for acontinuing period of 10 months at data cut-off. He still was notreceiving any secondary treatment after vaccination end. He wasvaccinated with MONTANIDE® as the only adjuvant (FIG. 8, Table 13).

TABLE 8 PSA Doubling Time in months Geometric Range Total % Mean of DTPSA DT prior vaccination in 19  8.3 1.5-44.8 months PSA DT at study endor at end of 18* 11.2 2.2-148  follow-up No change of PSA DT during 11 58 2.2-44.8 vaccination Increased PSA DT continuing at 4 21 end of studyNo change of PSA DT during 1 5 vacc but decline after Interim PSAdecline or DT 3 16 increase followed by DT decrease *PSA DT at study endor end of follow-up was not included for Pat. 5 due to PSA decline

TABLE 9 PSA stability with no rise greater than 10% from baseline PSAPSA_(baseline ng/ml) PSA_(end of study ng/ml)PSA_(end of follow up ng/ml) Months_(since baseline) pat 3 0.7 0.51 0.7331 pat 8 1.76 1.84 1.85 28

TABLE 10 Permanent increase of PSA DT in months during vaccination3^(th) DT during 1^(th) DT prior 2^(th) DT during vaccine vaccine monthsvaccine months months pat 3 9.8 −2.3 20.5 pat 8 6.6 148 pat 11 1.5 10.1pat 16 6.1 −2.7 14.4 geometric mean DT 4.9 25.8

TABLE 11 No change of PSA DT in months during vacc but decline after1^(th) DT prior vaccine 2^(th) DT during months vaccine months pat 5 3.2−20.2

TABLE 12 Interim PSA DT decline/stability in months followed byaccelerated rise 1^(th) DT prior 2^(th) DT during 3^(th) DT during4^(th) DT during vaccine vaccine vaccine vaccine months months monthsmonths pat 7 3.7 21.5 2.8 pat 15 1.3 25.8 −9.9 7.4 pat 17 10.2 −1.9 4.8

TABLE 13 Adjuvants and patient response. No PSA response (−), interimPSA fall and accelerated rise after (+/−), PSA DT increase (+) No Hyper-Gm adjuvants Response ALDARA ® Response thermia Response CSF ResponseRNA Response pat 1 − pat 3 + pat 13 − pat 4 − pat + 16 pat 2 − pat 7 +/−pat 10 − pat 6 − pat +/− 17 pat 5 − pat 8 + pat 12 − pat − 18 pat 9 −pat 11 + pat 14 − pat − 19 pat 15 +/−

Synthesis

The peptides were synthesized using a fully automatically in the EPS 221peptide synthesizer manufactured by Abimed. The synthesis programfollows the manufacturer's standard protocols. To the extent possible,the batch numbers of the reagent batches are registered for eachpeptide.

Processing to the Raw Peptide

The processing of the raw peptide was done by splitting off of thesynthesis resin and release of the side-chain protective groups byTFA/phenol/ethane dithiol/thioanisole/water (90/3.75/1.25/2.5/2.5,volume percent, respectively) 1 h or 3 h (peptides with arginine).Precipitation of the raw peptide in methyl-tert-butylether, washing withmethyl-tert-butylether and twice with diethylether, drying anddissolution of the peptide pellet in acetic acid. Another precipitationin diethylether, drying, resuspension in water, and freeze-drying.

Preparative HPLC

HPLC system Varian “Star,” chromatography column 250×10 mm C18 5 μm(Manufacturer Ziemer). Mobile solvent A: water with 0.1% TFA, mobilesolvent B: acetonitrile with 0.08% TFA. The gradient used for separationis oriented to the hydrophobicity of the peptide. The separated peptidefractions are freeze-dried.

Analysis

For each peptide, an HPLC chromatogram and a MALDI mass spectrum wererecorded to prove the identity (via the molar mass in the mass spectrum)and purity (via the peak areas in the HPLC chromatogram).

Synthetic Peptides and Stimuli

Synthetic peptides used for the stimulation and for functional testswere the HIV-derived epitope (HIV gag 164-181: YVDRFYKTLRAEQASQEV (SEQID NO: 65), negative control), PSMA 459-473: NYTLRVDCTPLMYSL (SEQ ID NO:64) and Survivin 97-111: TLGEFLKLDRERAKN (SEQ ID NO: 1). Staphylococcusenterotoxin B (SEB, Sigma-Aldrich, Taufkirchen, Germany) was used as apositive control stimulation for CD4⁺ T-cells in the Interferon-γELISPOT.

In vitro Amplification of Specific T-cells

Peripheral blood mononuclear cells from prostate carcinoma patients wereobtained at different time-points during vaccination and cryopreservedin 90% fetal calf serum and 10% DMSO in liquid nitrogen. After thawing,approximately 5×10⁶ cells were cultivated (24-well cell culture plate,Greiner Bio-One, Frickenhausen, Germany) in IMDM medium supplementedwith 50 U/ml Penicillin, 50 μg/ml Streptomycin (all Biowhittaker,Verviers, Belgium), 10% heat-inactivated human serum (c.c. pro,Neustadt, Germany) and 50 μM beta-mercaptoethanol at 37° C. and 7.5%CO₂. Pooled synthetic HLA-class II binding peptides were added at day 1,each at 5 μg/ml and the culture was supplemented with recombinant humanIL-2 (r-hIL2, R&D Systems GmbH, Wiesbaden, Germany) at days 2, 5, 7 and9 of the T-cell stimulation.

Enzyme-linked Immunosorbent Spot (ELISPOT) Assay

The functionality of expanded T-cells was tested in a standardInterferon-γ ELISPOT assay according to the recommendations of the CIMTMonitoring Panel. Briefly, cells were harvested after the 12 dayculture, washed, counted and seeded in culture medium on an ELISPOTplate (Millipore, Schwalbach, Germany). Between 0.15 and 0.25×10⁶ cellswere tested in duplicates or triplicates, in the presence of thesynthetic peptides at 2.5 μg/ml or SEB at 1 μg/ml. Production of IFN-γwas detected with a pair of specific monoclonal antibodies (1D1-k and7-B6-1, both Mabtech, Nacka Strand, Sweden) after 26 hour incubation at37° C. and 5% CO₂. ExtraAvidin-Alkaline Phosphatase and BCIP/NBTsubstrate (both Sigma-Aldrich) were added for 1 hour and 10 minrespectively. ELISPOT analysis was performed using ImmunoSpot readers(Series 3A and 5, Cellular Technology Ltd, Aalen, Germany).

Intracellular Cytokine Staining

Cells recovered from the ELISPOT were further cultivated in the presenceof 2 ng/ml r-hIL2 for nine additional days. After this re-stimulationperiod, effectors were harvested, washed and stimulated in a standardassay with the peptides at 5 μg/ml or PMA and Ionomycin (50 ng/ml and 1μM, respectively) in the presence of Golgi-STOP (BD Biosciences,Heidelberg, Germany) following the manufacturers instructions. Followingan incubation period of 6 hours, cells were washed in PBS 1% FCS 0.02%NaN₃ and stained with monoclonal antibodies (MoAb) CD4-APC-Cy7 (BDBiosciences) and CD8-PE-Cy7 (Beckman Coulter) for 20 min at 4° C. in thedark. After a washing step, cells were permeabilized 20 min withCytofix/Cytoperm reagent (BD Biosciences) then stained for intracellularcytokines for 30 min. MoAb used were IFN-γ-FITC, IL-10-PE (both BDBiosciences), IL-5-APC (Miltenyi Biotec, Bergisch Gladbach, Germany) andTNF-α-Pacific Blue (Biolegend, San Diego, Calif.). Cell acquisition wasperformed on a Cytometer Canto II using the software Diva and analysiswith FlowJo (BD Biosciences).

Example 5 Binding of BIR-11, BIR-12, and BIR-13 to HLA-A*0211

The objective of this analysis was to evaluate the affinity of BIR-004(ELTLGEFLKLDRERAKN (SEQ ID No: 2)) C-terminal peptides to the MHCmolecule coded by the HLA-A*0211 allele as this an allele with reportedcapacity to bind peptides with C-terminal asparagine residues. MHCligands with c-terminal N are not very frequent and to date only 66peptides with N in the C-terminus have been tested. The vast majority ofthese peptides are non-binders, however, there are a few exceptions:RLYNFSFLN (SEQ ID No: 66) binds strongly to A*0211 and also YADGGQWYN(SEQ ID No: 67) binds to A*021.

The tests clearly indicated that binding to HLA-A*0211 has been foundfor BIR-11 (C-terminal nonamer: KLDRERAKN (SEQ ID No: 68)) and BIR-13(C-terminal decamer: LKLDRERAKN (SEQ ID No: 69)) at higherconcentrations but not for BIR-12 (C-terminal octamer: LDRERAKN (SEQ IDNo: 70)). The positive control peptide (Sequence: FLPSDYFPSV (SEQ ID No:71)) showed clear binding properties.

Principle of Test

An assay was set up as follows: Stable HLA/peptide complexes consist ofthree molecules: HLA heavy chain, beta-2 microglobulin (b2m) and thepeptidic ligand. The activity of denatured recombinant HLA-A*0211 heavychain molecules alone can be preserved making them functionalequivalents of “empty HLA-A*0211 molecules.” When diluted into aqueousbuffer containing b2m and an appropriate peptide, these molecules foldrapidly and efficiently in an entirely peptide-dependent manner. Theavailability of these molecules is used in an ELISA-based assay tomeasure the affinity of interaction between peptide and HLA class Imolecule {Sylvester-Hvid, 2002 SYLVESTERHVID2002/id}.

Purified recombinant HLA-A*0211 molecules were incubated together withb2m and graded doses of the peptide of interest. The amount of denovo-folded HLA/peptide complexes was determined by a quantitativeELISA. Dissociation constants (K_(D) values) were calculated using astandard curve recorded from dilutions of a calibrant HLA/peptidecomplex. The deviance in the measurements was too big to give reliableK_(D) values, although it can be said that the K_(D) value for BIR13 isin the range of the positive control whereas the K_(D) value for BIR-11is higher. A lower K_(D) value reflects higher affinity to HLA-A*0211.

Binding-Scores of the nonamer BIR-11 and the nonamer BIR-11a againstseveral alleles using SYFPEITHI.

Allele- Allele Rel id name score score KLDRERAKD (SEQ ID NO: 72)KLDRERAKD  74 A*0301 0.45 20 KLDRERAKD  65 A*0201 0.42 15 KLDRERAKD  99B*1501  0.36 10 (B62) KLDRERAKD 334 A*0101 0.28 14 KLDRERAKN(SEQ ID NO: 68) KLDRERAKN  74 A*0301 0.45 20 KLDRERAKN  65 A*0201 0.4215 KLDRERAKN  99 B*1501  0.36 10 (B62) KLDRERAKN 334 A*0101 0.28 14

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The invention claimed is:
 1. An isolated nucleic acid sequence encoding:a peptide consisting of SEQ ID NO:
 3. 2. An expression vector comprisingthe isolated nucleic acid sequence of claim
 1. 3. An isolated host cellcomprising the expression vector of claim
 2. 4. The isolated host cellof claim 3, wherein said host cell is an antigen presenting cell.
 5. Theisolated host cell of claim 3, wherein said host cell is a dendriticcell.